Supplementary Materials for - Sciencescience.sciencemag.org/content/sci/suppl/2012/09/... · Supplementary Materials for ... Nenad Ban, Lars Malmström, Ruedi Aebersold* ... 0.2 mM

www.sciencemag.org/cgi/content/full/337/6100/1348/DC1

Supplementary Materials for

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

Franz Herzog, Abdullah Kahraman, Daniel Boehringer, Raymond Mak, Andreas Bracher, Thomas Walzthoeni, Alexander Leitner, Martin Beck, Franz-Ulrich Hartl,

Nenad Ban, Lars Malmström, Ruedi Aebersold*

*To whom correspondence should be addressed. E-mail: [email protected]

Published 14 September 2012, Science 337, 1348 (2012) DOI: 10.1126/science.1221483

This PDF file includes:

Materials and Methods Figs. S1 to S14 Tables S1 to S14 Boxes S1 to S9 References

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Materials and Methods

M1. Cell line generation and cell culture

Open reading frames (ORFs) of bait proteins (table S2) were retrieved in a pDONR223 vector

from the Gateway (Life Technologies, www.lifetechnologies.com) adapted human ORF

collection (horfeome v5.1, Open Biosystems, www.openbiosystems.com). 2A5E and SGOL1

were amplified from the MegaMan Human Transcriptome library (Agilent) and inserted into

pDONR223 vector by BP recombination.

ORFs were introduced by LR recombination into a destination vector that was constructed by

ligating the Gateway recombination cassette and an N-terminal His6-HA-StrepII-tag into the

polylinker of the pcDNA5/FRT/TO vector (Life Technologies). Flp-In T-REx HEK293 cells

(Life Technologies) containing a single genomic FRT site and expressing the tet repressor

protein were used to generate stable isogenic cell lines for the tetracycline inducible

expression of tagged bait proteins (fig. S1) (39).

HEK293 cells were grown in DMEM (Life Technologies, #11995-065) supplemented with

10% FBS (PAA Laboratories), 0.2 mM L-glutamine, 100 µg/ml hygromycin B and 15 µg/ml

blasticidin S (all Life Technologies) and were plated on 245x245 mm cell culture dishes

(Nunc). Protein expression was induced in medium lacking hygromycin and blasticidin by the

addition of 1 µg/ml tetracycline 24 hours prior to harvest. Cells were detached by pipetting,

washed twice with ice-cold PBS and cell pellets were frozen in liquid nitrogen.

M2. Protein complex purification and chemical cross-linking

Cells were resuspended in two pellet volumes of AP buffer [20 mM Tris-HCl pH 7.5, 150

mM KCl, 5% (v/v) glycerol, 0.1% (v/v) Tween-20 and 0.5 mM dithiothreitol] containing 2

µM avidin (IBA) and lyzed in a glass cell homogenizer (Sartorius). Cell debris was removed

by centrifugation at 16,000xg and the cleared lysate of 1 ml cell pellet was applied twice to

400 µl bed volume of Strep-Tactin sepharose (IBA) by gravity flow. Bound proteins were

washed three times with 2.5 ml AP buffer containing 2 µM avidin and eluted with four bed

volumes of AP buffer containing 2 mM biotin (Thermo Scientific, #2912). The recovered

proteins were immobilized on 150 µl bed volume Ni-NTA agarose (Qiagen) by incubation in

a 15 ml Falcon tube for 30 min at 4°C with end-over-end rotation. Beads were washed three

times with 10 ml XL buffer [25 mM HEPES pH 8.0, 300 mM KCl, 5% (v/v) glycerol]

containing 0.05% (v/v) Tween-20 and transferred into a 1.5 ml Eppendorf tube.

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An equimolar mixture of isotopically light (d0) and heavy (d12) labeled disuccinimidyl

suberate (DSS; Creative Molecules, www.creativemolecules.com) was dissolved in

dimethylformamide (DMF, Thermo Scientific) at a concentration of 50 mM. The stock

solution was further diluted in water in order not to exceed a final DMF concentration of 2%

(v/v) in the reaction mixture. The cross-linking reaction was performed by resuspending the

protein bound Ni-NTA beads in two bed volumes of XL buffer and adding the appropriate

amount of DSS. The reaction mixture was incubated with mixing at 900 rpm for 30 minutes at

37°C. Cross-linking was quenched by the addition of ammonium bicarbonate to a final

concentration of 50 mM for 10 minutes at 37°C.

The appropriate DSS concentration was determined for several affinity-purified protein

complexes by incubating 5 µl protein bound matrices with increasing concentrations of DSS

(fig. S2). Depending on the bait protein, 2-4 ml HEK293 cell pellet was used as starting

material yielding 3-20 µg total protein at 0.1-0.4 µg/µl for the identification of cross-linked

peptides by mass spectrometry.

Proteins were visualized by immuno-blotting and silver staining as described elsewhere (19,

40).

M3. Enrichment and mass spectrometric analysis of cross-linked peptides

Subsequent to quenching, Ni-NTA agarose was resuspended in one bed volume of 50 mM

ammonium bicarbonate and proteins were denatured by the addition of four bed volumes 8 M

urea (Sigma). Cross-linked proteins were reduced with 5 mM tris(2-carboxyethyl)phosphine,

(TCEP,Thermo Scientific) at 37°C for 15 min and alkylated with 10 mM iodoacetamide

(Sigma-Aldrich) for 30 min at room temperature in the dark. Proteins were digested with lysyl

enodpeptidase (Wako) at an enzyme-substrate ratio of 1 to 50 (w/w) at 37°C for 2 hours.

After diluting the solution with 50 mM ammonium bicarbonate to 1 M urea a second digest

with 1/50 (w/w) trypsin (Promega) was performed at 37°C overnight. Peptides were acidified

with 1% (v/v) trifluoroacetic acid (TFA, Sigma-Aldrich) and purified by solid-phase

extraction (SPE) using C18 cartridges (Sep-Pak, Waters). The SPE eluate was dried by

vacuum centrifugation and reconstituted in 20 µl of SEC (size exclusion chromatography)

mobile phase (water/acetonitrile/TFA, 70:30:0.1) and 15 µl was injected on a GE Healthcare

ÄKTAmicro chromatography system. Peptides were separated on a Superdex Peptide PC

3.2/30 column (300 x 3.2 mm) at a flow rate of 50 µl min-1 using the SEC mobile phase.

Fractions of 100 µl were collected every two minutes.

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Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analysis was

carried out on an Eksigent 1D-NanoLC-Ultra system connected to a Thermo LTQ Orbitrap

XL mass spectrometer (LIT-Orbitrap, linear ion trap-orbitrap) equipped with a standard

nanoelectrospray source. SEC fractions were reconstituted in mobile phase

(water/acetonitrile/formic acid, 97:3:0.1). A volume corresponding to 1 ug peptide was

injected onto a 11 cm x 0.075 mm I.D. column packed in house with Michrom Magic C18

material (3 µm particle size, 200 Å pore size). Peptides were separated at a flow rate of 300 nl

min-1 ramping a gradient from 5% to 35% mobile phase B (water/acetonitrile/formic acid,

3:97:0.1) (13).

Ion source and transmission parameters of the mass spectrometer were set to spray voltage =

2 kV, capillary temperature = 200 °C, capillary voltage = 60 V and tube lens voltage = 135 V.

The mass spectrometer was operated in data-dependent mode, selecting up to five precursors

from a MS1 scan (resolution = 60,000) in the range of m/z 350-1,600 for collision-induced

dissociation (CID). Singly and doubly charged precursor ions and precursors of unknown

charge states were rejected. CID was performed for 30 ms using 35% normalized collision

energy and an activation q of 0.25. Dynamic exclusion was activated with a repeat count of 1,

exclusion duration of 30 s, list size of 300 and a mass window of ±50 ppm. Ion target values

were 1,000,000 (or maximum 500 ms fill time) for full scans and 10,000 (or maximum 200

ms fill time) for MS/MS scans, respectively.

M4. Generation of the database for the xQuest search of cross-link spectra

Mass spectrometric analysis of the non-cross-linked protein complexes by a Thermo LTQ

Orbitrap XL instrument was used to generate a database for the xQuest search of cross-link

spectra. Thermo Xcalibur .raw files were converted into the open mzXML (41) format by

msconvert (42). Tandem mass spectra were searched against the UniProtKB/Swiss-Prot

protein database (release 2010_06) and proteins were identified using the X!Tandem search

algorithm (43). Search results were evaluated on the Trans Proteomic Pipeline (TPP v4.5)

using PeptideProphet (44) and ProteinProphet (45). The xQuest databases established from

the respective non-cross-linked affinity-purifications included the 40 proteins with the highest

number of spectral counts (table S3).

M5. Identification of cross-link spectra by xQuest and manual validation

Cross-linked peptides and peptide mono-links were identified by the dedicated search engine,

xQuest (18). Tandem mass spectra of precursors triggered within 2.5 min of each other and

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displaying an isotopic mass shift of 12.075321 Da (DSS-d12 - DSS-d0) (46, 47) and a charge

state of 3+ to 8+ were paired. These spectra were searched against the preprocessed .fasta

database.

The xQuest search parameters were set as follows: maximum number of missed cleavages

(excluding the cross-linking site) = 2, peptide length = 4-40 amino acids, fixed modifications

= carbamidomethyl-Cys (mass shift = 57.021460 Da), variable modifications = oxidation-Met

(mass shift = 15.99491), mass shift of the light cross-linker = 138.068080 Da, mass shift of

mono-links = 156.078644 and 155.096428 Da, MS1 tolerance = 15 ppm, MS2 tolerance = 0.2

Da for common ions and 0.3 Da for cross-link ions, search in ion-tag mode.

The theoretical candidate spectra assigned to the experimental spectrum were scored

according to the quality of the match. The cross-link candidates were filtered by the MS1 mass

tolerance window (-4 to +7 ppm) and the ∆score (≥ 15%) indicating the relative score

difference to the next ranked match.

All spectra passing the filtering step were manually validated. The minimum xQuest score

threshold for manual validation was estimated by a target-decoy approach (table S13).

Identifications were only considered for the final result list once both peptides had at least

four bond cleavages in total or three adjacent ones and a minimum length of six amino acids

(fig. S3). Only those cross-links containing one peptide of five amino acids and fulfilling the

filtering and manual validation criteria were included at a xQuest score >29.

M6. Analysis of protein interaction data

Proteins co-purifying with the bait protein were separated in contaminating proteins and

interactors by applying a spectral count-based strategy. The average spectral counts were

calculated from at least three replicate affinity-purifications of the non-cross-linked bait

proteins and of His6-HA-StrepII-eGFP as a control (table S2). The ratio of the average

spectral counts for each protein in the bait and control purification was calculated. A ratio of

100 was assigned to proteins not detected in the eGFP purification. Proteins identified in all

replicate purifications of a bait protein and present at a ratio >6 were classified as interactors

(table S3), which were selected for assembly of the protein–protein interaction network model

using Cytoscape 2.8.1 (www.cytoscape.org) (Fig. 2A).

M7. Subunit stoichiometry by label-free quantification

Protein complexes associated with 2ABG were purified via its His6-HA-StrepII-tag from

HEK293 cells in three biological replicates and analyzed by mass spectrometry. Raw data

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files were loaded into Progenesis LC-MS (version 4.0, Nonlinear Dynamics) in profile mode

and total ion chromatograms were aligned using the automatic alignment function. Peptide

features were identified by importing pep.xml files containing peptide identifications from

X!Tandem searches. Protein abundances were calculated from the sum of the precursor

intensities of all proteotypic peptides.

To account for differences in yield between purifications, protein abundances were first

normalized to the abundance of the bait protein. To calculate the subunit stoichiometry,

protein abundances were then normalized to the respective molecular weights of the proteins.

M8. Pull-down binding assay

R155, K158 and K163 of IGBP1, identified at the IGBP1-PP2A interface by computational

protein-protein docking, were mutated to alanines. Single (R155A, K158A and K163A) and

double mutations (R155A/K163A, K158A/K163A, and R155A/K158A) were generated by

site-directed mutagenesis (QuikChange, Stratagene) using the IGBP1 destination clone

(chapter M1) as template DNA. HEK293 cells inducibly expressing N-terminally His6-HA-

StrepII-tagged wild-type or mutant IGBP1 were generated as described (chapter M1). IGBP1

protein was isolated from HEK293 cell lysates by a single StrepII-tag pull-down. Proteins in

the biotin eluate were separated by SDS-PAGE and the levels of bound PP2A catalytic

subunits were visualized by immuno-blotting (35).

M9. Cryo-electron microscopy of 2ABG bound TRiC chaperonin

For the general views of the TRiC complex, we prepared EM samples from the affinity-

purified 2ABG-TRiC complex by conventional negative staining (48). Briefly, a solution of

2ABG-TRiC complex was adsorbed to a thin carbon film and stained with 2% (w/v) uranyl

acetate solution for 2 min. Images were obtained at 60,000× magnification on a Fei F20

electron microscope with a Gatan US 4000 CCD camera. Images of 2,130 single particles in a

cross-linked sample and 2,789 images of a control sample without cross-link treatment were

semi automatically selected using Boxer (49). A 'reference-free' alignment and multivariate

statistical analysis scheme was used for image classification (20-30 images per class) with the

Imagic-5 software (50).

For three-dimensional reconstruction of the 2ABG-TRiC complex, images were taken at

82,000× magnification under low-dose conditions at 3-5 micron defocus with a Fei F20

electron microscope on a Gatan UltraScan 4000 CCD camera (15 micron pixel size). Images

were collected semi-automatically using a SerialEM script (51). A total of 5,974 single-

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particle images were CTF corrected (52) computationally coarsened to a final pixel size of

3.64 Å and used for image processing with the Imagic-5 software (50). After a 'reference-free'

alignment procedure (53), images were subjected to a multivariate statistical analysis (54) and

classification. The class averages were used for three-dimensional structure determination by

the angular reconstitution approach (55). The down filtered structure of the Methanococcus

maripaludis chaperonin in the half open conformation was used for the initial angle

assignment of the class averages (56). In the refinement cycles, C8 point group symmetry was

applied to the three-dimensional reconstruction. The resolution of the structure estimated by

the Fourier shell correlation (FSC) function was found to be 23 Å using the 0.5 criterion.

M10. Hybrid structural modeling of the PP2A interaction network

Structural analysis by established high resolution techniques like X-ray crystallography or

Nuclear Magnetic Resonance (NMR) spectroscopy was only accomplished for a subset of

multi-subunit protein complexes. Similarly, such complexes are not amenable to pure

computational molecular modeling techniques, due to their size and complexity (57).

Hybrid or data driven modeling techniques are complementary modeling strategies that

combine experimental data with computational modeling algorithms in order to gain insights

into structural features of otherwise intractable protein complexes. Although, they do not

necessarily provide high-resolution images of the complexes, they do allow to propose

hypotheses on the structural mechanisms of proteins or to advise targeted follow-up

experiments like mutagenesis studies on predicted binding interfaces (58).

A hybrid modeling strategy is characterized by the availability of various experimental data at

different resolution, where each dataset carries only limited amount of structural information.

The goal in hybrid modeling is to collectively integrate the data into a molecular modeling

framework such that the calculations converge towards an ensemble of protein structures that

are likely candidates for the native protein complex (59).

In this study, mainly two types of experimental data were employed. First, protein structures

from the Protein Data Bank (PDB) (60) and secondly, chemical cross-link data. The former

was used as structural templates or starting structures for the modeling simulations. The latter

was integrated as distance restraint or distance filter. Distances between cross-linked amino

acids were calculated for each predicted model with a Solvent Accessible Surface (SAS)

distance measure as implemented in our software Xwalk (chapter M10.1.1). ROSETTA was

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chosen as a molecular modeling framework. It is well known for de novo structure prediction,

comparative modeling and protein docking, performing among the top scoring modeling

algorithms in the CASP and CAPRI challenges (61, 62).

M10.1. Methods and workflows for hybrid modeling

The forthcoming chapters give detailed descriptions on Xwalk, ROSETTA applications,

auxiliary methods and parameters used during our hybrid modeling calculations.

M10.1.1. Xwalk

The common distance measure for cross-link data in molecular modeling calculations has

been the Euclidean distance. The problem associated with the Euclidean distance is that its

linear distance vector frequently penetrates the protein surface, which a cross-linker molecule

is unlikely to imitate. The inappropriate representation of cross-link data by the Euclidean

distance measure can cause twice as many false positive validations of cross-links than a non-

linear distance measure (63). We have therefore developed a new computer program called

Xwalk (63) to calculate Solvent Accessible Surface (SAS) distance, which corresponds to the

length of the shortest path between two cross-linked amino acids, where the path must not

penetrate the protein surface, circumvent molecular barriers and bridge clefts and cavities (fig.

S6C). Thus, SAS distance calculations mimic the flexibility of cross-linker molecules and

attempt to approximate their position on the protein surface without explicitly modeling the

cross-linker molecule (64). To account for wrong side-chain rotamers in a model, all side

chain atoms except Cβ are removed prior to the shortest path calculation and the radius of the

solvent probe sphere is increased to 2.0 Å.

Due to its superior filter efficiency as indicated by the larger number of detected false positive

predictions (table S10) the SAS distance measure was preferred as a post-modeling filter in all

model predictions. An exception was made to the 2ABG-TRiC complex (chapter M10.2.5),

where the coordinate uncertainty in the protein models did not justify the application of SAS

distance calculations.

SAS distances between Cβ atoms of cross-linked amino acids were calculated for all

predicted models using the command-line flags listed in box S1. In addition, Xwalk was also

employed to calculate Euclidean distances for validation purposes using the command-line

flags in box S2 (chapter M10.2.1).

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M10.1.2. Modeling of cross-link distances

In our modeling calculations, cross-links between lysine residues were integrated into a

structural model in two ways. First, the Euclidean distances between Cβ-Cβ atoms of the

cross-linked lysine residue pairs were added as distance restraints to ROSETTA’s scoring

function. The SAS distance could not be used, as an implementation of the Xwalk shortest

path algorithm (chapter M10.1.1) was missing in ROSETTA. In addition, the shortest path

algorithm is computationally expensive, making it ill-suited for fast conformational sampling

calculations. Using Cβ-Cβ distances in modeling calculations accounts for the direction of the

lysine side chain which is largely independent of side chain rotamers. The restraints were

modeled as a flat-harmonic function with x0 = 15, standard deviation = 0 and tolerance = 15,

driving the conformational sampling in the various ROSETTA protocols towards models that

conformed to our cross-link data. Second, cross-links were applied as post-modeling distance

filters to separate the large number of false positive predictions that might also be located at

deep local energy minima. A predicted model passed the distance filter once the Cβ-Cβ

distances measured between the cross-linked lysine residues were below a maximum distance

threshold. For Euclidean distance filters, the threshold was set to 30.0 Å (11.4 Å N-N distance

of DSS + 2 x 6.0 Å Cβ-Nε distance of lysine + flexibility of the protein backbone).

As SAS distances are of equal length or longer than Euclidean distances, the maximum SAS

distance threshold for a valid cross-link was increased to 34.0 Å. The 34.0 Å SAS distance

threshold was considered to be equivalent to the 30.0 Å Euclidean distance threshold as ≥

90% of cross-links exhibited a value below this cut-off (fig. S5).

M10.1.3. ROSETTA applications

In this study, all modeling calculations were performed using the ROSETTA molecular

modeling suite (62, 65). All applied protocols were available in the public releases of

ROSETTA starting from version 3.1, with the exception of the protocol nonlocal, which was

downloaded from ROSETTA’s trunk at revision 42791.

Protein structure prediction calculations required fragment files (66), which were generated

using the ROBETTA server (67), available at http://robetta.bakerlab.org. Secondary structure

predictions were carried out using PSIPRED (68). Sequence alignments between the target

and the template proteins were generated using needle from the EMBOSS package v6.2.0 (69)

with default command-line flags, a gap open penalty of 10.0 and a gap extension penalty of

0.5. To drive the conformational sampling in the various ROSETTA protocols towards models

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that conform to cross-links, a list of Cβ-Cβ cross-link Euclidean distance restraints were

supplemented to the ROSETTA scoring function (chapter M10.1.2).

M10.1.3.1. Loop-modeling

Loop-modeling calculations were performed using the ROSETTA loopmodel protocol (70),

with the command-line flags displayed in box S3. As a loop-closure algorithm, the ROSETTA

implementation of the cyclic coordinate descent (71) was chosen, allowing for modeling of

terminal loop regions.

At least 3,000 loop models were generated using cross-link distance restraints in the

ROSETTA scoring function. Loop models having Euclidean distances ≤ 30.0 Å for the

majority of cross-links were selected and hierarchically clustered based on the Cα Root Mean

Square Deviation (RMSD) using the hclust function in R v2.13.1, the complete clustering

method and a cluster height of 10.0 Å. Models having the lowest ROSETTA energy score

within each cluster were selected as best models. RMSD calculations were conducted using

the Kabsch algorithm as implemented in the CleftXplorer code library (72, 73).

M10.1.3.2. Comparative modeling

Comparative models of target proteins were generated using the ROSETTA threading and

relax protocol via the minirosetta application (74) and the command-line flags in box S4.

For each target protein 200 models were generated from ROBETTA server fragments,

PSIPRED secondary structure assignments, a template protein structure from the PDB and

intra-protein cross-link distance restraints. The model with the largest number of cross-links

having SAS distances ≤ 34.0 Å was selected as the best model. If several models conformed

to the same number of cross-links with SAS distances ≤ 34.0 Å, the model with the smallest

Cα RMSD to its template was chosen. RMSDs were calculated using the Kabsch algorithm in

CleftXplorer.

M10.1.3.3. De novo modeling with local structure information

Two-domain proteins of unknown structures and with a homologous protein structure for one

of the domains available were modeled using the ROSETTA nonlocal protocol and the

command-line flags in box S5.

150,000 models of the full-length protein were generated from ROBETTA server fragments,

PSIPRED secondary structure assignments, a template protein with known structure and intra-

protein cross-link distance restraints. Models conforming to a maximum number of cross-

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links with SAS distances ≤ 34.0 Å and showing a RMSD ≤ 10.0 Å to the template structure

were selected as best models. RMSD calculations were carried out using the Kabsch

algorithm in CleftXplorer.

M10.1.3.4. Cross-link driven protein-protein docking

Binary protein-protein docking calculations were performed using the ROSETTA

docking_protocol application (26) and the command-line flags in box S6.

Approximately 350,000 models were generated with random orientations between both

binding partners in low-resolution using inter-protein cross-link distance restraints. In low-

resolution, ROSETTA replaces all amino acid side chains with pseudo centroid atoms and

employs a simple scoring term to rate a docking model (26, 62). Models displaying Euclidean

distances ≤ 30.0 Å for all inter-protein cross-links were further analyzed for the number of

cross-links fulfilling a SAS distance ≤ 34.0 Å. The models with the highest number of intra-

and inter-protein cross-links passing the SAS distance filter and having solvent accessible

mono-linked residues. were subsequently tested for their binding interface size using the

Naccess program (75). Only models having interface sizes ≥ 900 Å2 were selected and

converted to full-atom models using the docking_protocol application and the command-line

flags in box S7. Finally, 300 models with the shortest average SAS distance for all

conforming cross-links were hierarchically clustered with the complete clustering method and

a cluster height of 15 Å (chapter M10.1.3.1). The clusters members within the largest clusters

with the lowest ROSETTA score were chosen as best docking models.

Using the Xwalk SAS distance measure, we also included intra-protein cross-links and mono-

links as a post-modeling filter to the docking workflow, although their filtering effect was

minor in this study (table S10). The use of these modifications is based on the assumption that

both must be surface-exposed and not buried in interfaces. Predicted models with the shortest

path for an intra-protein cross-link or a mono-linked residue interfering with the interface

were considered as invalid models and filtered out. This assumption is valid for stoichiometric

and homogeneous protein complexes. Affinity-purified bait proteins may be isolated as a

singular protein or in complex with its binding partners. It is thus likely that intra-protein

cross-links and mono-links on bait proteins overlap with the interface of binding partners.

This is negligible for intra-protein cross-links and mono-links identified on prey proteins. For

this reason, intra-protein cross-links and mono-links exclusively detected on prey proteins

were applied as post-modeling filter.

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M10.2. Application of Hybrid Modeling to the PP2A Interaction Network

The next chapters describe various hybrid-modeling workflows applied to protein complexes

of the PP2A interaction network.

M10.2.1. Cross-link Evaluation on X-ray Structures and Comparative Models

Previous studies used the Euclidean distance between the Cɑ atoms of cross-linked amino

acids as a measure to validate cross-link data on protein structures (5, 76). In order to provide

distance distributions comparable to other studies, we determined the Euclidean distance

between Cɑ atoms of the cross-linked lysine residues. Cβ coordinates were preferred for

modeling calculations (chapter M10.1.2).

Experimental structures for the validation of inter- and intra-protein cross-links were retrieved

from the PDB and the PDB identifiers were extracted from UniProt (77). In case of several

PDB identifiers, all crystal structures were retrieved and only the shortest Cα-Cα distance

within all PDB structures was reported.

In addition to the few X-ray structures of PP2A network proteins available in the PDB, we

constructed comparative models for additional proteins that had a close sequence homolog in

the PDB. The constructed models were used as starting structures for e.g. docking

calculations (chapter M10.2.3) but also allowed us to evaluate additional 275 cross-links

within our cross-link dataset. As all target proteins had a sequence identity of ≥ 50% to their

template proteins (table S6), the expected error in their predicted Cɑ coordinates was about

1.0 Å (78), which was considered as sufficiently accurate for validation purposes.

Cross-links on subunits of the PP2A trimeric complex were mapped on the crystal structures

of the human/mouse PP2A complex (PDB entry 3FGA) and the human PP2A complex (PDB

entry 3DW8) as shown in fig. S4, A and B. Subunits in 3FGA and 3DW8 were also used as

templates for the comparative modeling of the scaffold subunit 2AAB, the regulatory subunits

2ABA, 2ABG, 2ABD, 2A5A, 2A5D, 2A5E and the catalytic subunit PP2AB (table S6). The

comparative modeling protocol (chapter M10.1.3.2) was applied, except for 2ABA and

2ABG, where models consistent with most of the cross-links were misfolded (2ABA: 19.6 Å

RMSD to 3DW8-B, 17/17 valid cross-links; 2ABG: 22.9 Å RMSD to 3DW8-B, 15/18 valid

cross-links). For these two proteins the models with the lowest Cα RMSD to the template

structure 3DW8-B were chosen. In all other cases, the selected best models were among the

lowest scoring models in the comparative modeling calculations.

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Comparative models of binary complexes were generated by analogy (79) through

superposing Cα atoms of the models on corresponding Cα atoms of the template structures in

3FGA or 3DW8 using the Kabsch algorithm in CleftXplorer. (fig. S4, A and B). Cross-links

on TRiC were mapped to the open conformation of TRiC (Fig. 4A and fig. S4C), which was

computed from comparative models of all eight subunits (chapter M10.1.3.2) using the

thermosome subunit alpha in its closed conformation as template (PDB entry 1Q2V). The

comparative modeling was followed by separating the coordinates of the apical domains from

coordinates of equatorial and intermediate domains and superimposing them by the program

LSQMAN (80) onto the crystal structure of bovine TRiC in the open conformation (35) (PDB

entry 2XSM) according to the reported subunit topology (33, 34).

From the list of 357 cross-links (287 intra-protein and 70 inter-protein) that had coordinates in

one of the crystal structures or comparative models, 327 cross-links or 92% (270 intra-protein

and 57 inter-protein) spanned a Euclidean distance between their Cɑ atoms of ≤ 30.0 Å (Fig.

2C and fig. S5). Similarly, 289 cross-links (240 intra-protein and 49 inter-protein) had a SAS

distance ≤ 34.0, which corresponds to 81% of cross-links. Furthermore, from 568 measured

mono-links, 290 had structural coordinates of which six were not solvent accessible.

According to the Shapiro-Wilk normality test, none of the distance distributions followed a

normal distribution with p-values ≤ 0.00025 (Fig. 2C and fig. S5). At the same time, the

distance distributions of all intra-protein and inter-protein cross-links were significantly

different with a p-value = 1.8x10-7 for Euclidean distances and a p-value of 1.6x10-4 for SAS

distances, according to the Wilcoxon rank sum tests (fig. S5E). Despite the large number of

cross-links found in this study, the data set constituted only about 15% of the potential cross-

links (table S14). A lysine residue pair was regarded as potentially cross-linkable, if its SAS

distance was ≤ 34.0 Å.

The average absolute solvent accessible surface area of cross-linked lysine residues was found

to be 98.60 Å2. Of 405 lysine residues, 12 (or 3%), were found to be not solvent accessible

with relative solvent accessible surface areas below 5%. The large majority of the inaccessible

lysine residues were found in the TRiC chaperonin complex, with five lysine residues being in

the inter-ring interface, two residues in the intermediate plane and two lysine residues in one

of the apical domains. As the TRiC chaperonin is known to undergo large conformational

changes upon substrate binding, these residues could become solvent accessible during

conformational rearrangements indicating minor inaccuracies in our current TRiC model.

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M10.2.2. Generation of Full-length Models of IGBP1

For human IGBP1 no structural coordinates were available in the Protein Data Bank (PDB).

Coordinates existed for the N-terminal domain of its mouse homolog in the PDB entry 3QC1.

For the C-terminal domain no homology was identified in the PDB using the HHpred

webserver (81).

Full-length models of IGBP1 were generated by de novo modeling with local structure

information on the N-terminal domain as described in chapter M10.1.3.3.

In total, 150,000 models of IGBP1 were generated. 190 models displayed a SAS distance ≤

34.0 Å for at least 60 out of 65 intra-protein cross-links. Of the selected 190 models five had

an RMSD ≤ 10.0 Å between their N-terminal domain and the template structure 3QC1

(referred to as IGBP1_1 to IGBP_5). Euclidean distances and SAS distances for IGBP1_1 are

listed in table S7. Despite the large number of intra-protein cross-links and extensive

modeling, it was not possible to converge the modeling to a single fold for the C-terminal

domain (fig. S6). The average Cα RMSD for the C-terminal domain in all 190 models and in

the selected five models was 26.5 Å and 17.9 Å, respectively.

M10.2.3. Docking of IGBP1 to the catalytic subunits of PP2A and PP4

Initial docking calculations were performed between either of the five selected IGBP1 models

and the structure of PP2AA or PP4C. PP4C was comparatively modeled using the structure of

human PP2AA (PDB entry 2IE4) as a template (table S6) (chapter M10.1.3.2). Prior to

docking calculations, the crystal structure of PP2AA (PDB entry 3FGA, chain C) was relaxed

in five cycles by the ROSETTA relax application with the command-line arguments listed in

box S9. All docking calculations were performed as described in chapter M10.1.3.4.

PP2AA and PP4C are homologous with a sequence identity of 63.5% (table S6). Docking

calculations were expected to result in similar predicted interfaces with similar orientations of

the catalytic subunits, PP2AA and PP4C, with respect to IGBP1 (79, 82). We found that

docking models of PP2AA and PP4C with IGBP1_1 were more similar, exhibiting RMSD

values down to 1.8 Å than with the other four IGBP1 models revealing RMSD values higher

than 8.0 Å. The docking models with IGBP1_1 were selected for further analysis and we refer

to IGBP1_1 as IGBP1.

To filter the output of the initial docking calculations we used 11 intra-protein cross-links,

seven inter-protein cross-links and 10 mono-links for the IGBP1-PP2AA complex and four

intra-protein cross-links, three inter-protein cross-links and eight mono- for the IGBP1-PP4C

15  

complex as restraints. Of about 350,000 docking models 1,075 IGBP1-PP2AA and 1,170

IGBP1-PP4C models conformed to 27 out of 28 restraints and to 14 out of 15 restraints,

respectively, and had a binding interface size ≥ 900Å2 (table S10).

The 1,075 IGBP1-PP2AA and 1,170 IGBP1-PP4C docking models clustered into 237 and 212

groups. The models with the lowest ROSETTA score within each of the 237 and 212 clusters

of IGBP1-PP2AA and IGBP1-PP4C were plotted in Fig. 3A and fig. S7C, respectively. The

300 models with the shortest average SAS distances out of the 1,075 IGBP1- PP2AA or 1,170

IGBP1-PP4C docking models clustered into 70 or 74 groups, respectively. The four largest

clusters of IGBP1-PP2AA and IGBP1-PP4C contained a total number of 37 and 36 docking

models, respectively. We refer to these models and clusters as TOP4 models and TOP4

clusters, respectively. The models with the lowest ROSETTA score within each of the TOP4

clusters of IGBP1-PP2AA and IGBP1-PP4C were plotted in Fig. 3B and fig. S7E,

respectively. Inter-protein Euclidean and SAS distances for the TOP4 model of IGBP1-

PP2AA and IGBP1-PP4C with the shortest average SAS distance is listed in tables S8 and S9,

respectively.

To assess the performance of our docking workflow, we first tested the efficiency of the SAS

distance filter on the IGBP1-PP2AA complex. 14,417 models of all 344,910 models passed

the Euclidean distance filter with seven inter-protein cross-links. Applying the SAS distance

filter resulted in an additional decrease of the number of models with 4,148 models passing

the SAS distance filter (table S10). In contrast to the Euclidean distance, the Xwalk SAS

distance measure enabled the use of intra-protein cross-links and mono-links in the filtering

protocol (table S10 and chapter M10.1.3.4). Selecting and clustering the 300 models out of

the 14,417 models with the shortest average Euclidean distance for the seven inter-protein

cross-links, resulted in TOP4 models with IGBP1 binding sites similar to models of the TOP4

clusters using the SAS distance measure (fig. S8, A and B). Despite displaying similar IGBP1

binding sites, the orientation of IGBP1 was distinct with an average Cα RMSD of 36.2 Å

between both sets of lowest scoring TOP4 cluster models.

To test the effect of cross-link distance restraints on docking results, an additional docking

experiment was conducted without any experimental distance information. We performed a

pure computational ab initio docking study with IGBP1 and PP2AA, but omitting distance

restraints from the ROSETTA docking_protocol scoring function and from the subsequent

filtering procedure. The docking calculations were initiated by a global sampling stage at

16  

which 349,995 models were generated whereby the entire protein surfaces of both binding

partners were sampled. The 1000 models with the lowest energy score were selected and

filtered to have a binding interface size of ≥ 900 Å2. The four lowest scoring models were

further selected for a local-refinement docking run, where 5000 models each were generated

by translating and rotating one binding partner by maximum ±3.0 Å and ±8º, respectively.

The 500 lowest scoring models from the local-refinement stage were again filtered for having

a binding interface size ≥900 Å2 and hierarchically clustered based on their mutual RMSD

values with an RMSD cut-off value of 20.0 Å. The lowest scoring models in the final 10

clusters revealed an IGBP1 binding site on PP2AA which is opposite to the interface

identified by our constrained workflow (fig. S8C), highlighting the importance of

experimental distance information for IGBP1-PP2AA docking. The average Cα RMSD

between the lowest scoring representatitives of the 10 clusters and the TOP4 clusters using the

SAS distance constrained docking workflow was 78.0 Å.

M10.2.4. Prediction of the IGBP1-PP2AA and IGBP1-PP4C protein-protein interfaces

For the prediction of amino acids forming the interface between IGBP1 and PP2AA or PP4C,

a selection of docking models was examined for the relative frequency of amino acids

participating in the predicted interfaces following the principle of the atom contact frequency

of Hwang et al. (82).

Based on the frequency analysis including all TOP4 models, K163 (IGBP1) and E37

(PP2AA) in IGBP1-PP2AA and K163 (IGBP1) and E34 (PP4C) in IGBP1-PP4C were

identified as the most frequent interface-residues (Fig. 3C; figs. S7F, S9, S10; and table S11).

The frequency analysis including all 300 models with the shortest average SAS distances

detected the same amino acids for IGBP1-PP2AA (fig. S7B) and for PP4C and revealed R155

as the most frequent interface-residue of IGBP1 in docking calculations with PP4C (fig. S7D).

The most frequent interface-residues of IGBP1-PP2AA and IGBP1-PP4C docking models are

listed in table S11.

M10.2.5. Localization of 2ABG in a 2ABG-TRiC complex by inter-protein cross-links

The location of 2ABG within the open conformation of human TRiC (Fig. 4C) was

determined by a distance minimization method using a selection of four distance restraints

which linked predicted β-sheets of the WD40 propeller of 2ABG to TRiC subunits (fig. S13

and table S12). The 15 cross-links to extended and potentially flexible loop regions of 2ABG

17  

were excluded from the distance calculations. For visualization purposes, the β-hairpin arm

from 2ABG ranging from E122 to V160 was removed and all atomic clashes were ignored.

As a starting point for distance minimization, the comparative model of 2ABG was placed at

the apical domain of TRiC. A series of translational moves was carried out to slide the

comparative model 50 Å along the pseudo 8-fold symmetry axis in 1.0 Å steps towards the

equatorial domain. Each translational move was accompanied by a full rotational move in one

degree steps. At each step, the average Euclidean distance of all four cross-links was

computed. The location of 2ABG within the TRiC cavity corresponded to the lowest global

average Euclidean distance calculated from the four selected inter-protein cross-links (Fig.

4C). Inter-protein distances between TRiC and 2ABG for the lowest average Euclidean

distance are listed in table S12.

M10.2.6. Auxiliary Modeling Calculations

Homology models of MOB4, MST4, STRN3 and STRN4 were generated using the full

UniProt sequence and the HHpred webserver (81). Templates for the MODELLER software

(83) at the HHpred webserver were yeast MOB1 (PDB entry 2HJN, chain A), human MST3

(PDB entry 3A7I, chain A), the C-terminal WD domain of mouse apoptotic protease-

activating factor Apaf1 (PDB entry 3SFZ, chain A) and the WD domain of the Arabidopsis

thaliana G-protein subunit RACK1A (PDB entry 3DM0, chain A), respectively. Unstructured

N- and C-termini of the resulting models for MST4, STRN3, and STRN4 were trimmed

manually at positions displayed in Fig. 3E. Missing loop regions in the human crystal

structure of SET (PDB entry 2E50) (31) and the N-terminal loop-region of SGOL1 were

constructed with ROSETTA’s loop modelling protocol (chapter M10.1.3.1) and selected for

the conformation with the lowest energy scores.

18  

Supplementary references

39. T. Glatter, A. Wepf, R. Aebersold, M. Gstaiger, Mol Syst Biol 5, 237 (2009).

40. F. Herzog, J. M. Peters, Methods Enzymol 398, 175 (2005).

41. P. G. Pedrioli et al., Nat Biotechnol 22, 1459 (Nov, 2004).

42. D. Kessner, M. Chambers, R. Burke, D. Agus, P. Mallick, Bioinformatics 24, 2534

(Nov 1, 2008).

43. R. Craig, R. C. Beavis, Bioinformatics 20, 1466 (Jun 12, 2004).

44. A. Keller, A. I. Nesvizhskii, E. Kolker, R. Aebersold, Analytical chemistry 74, 5383

(Oct 15, 2002).

45. A. I. Nesvizhskii, A. Keller, E. Kolker, R. Aebersold, Analytical chemistry 75, 4646

(Sep 1, 2003).

46. D. R. Muller et al., Analytical chemistry 73, 1927 (May 1, 2001).

47. J. Seebacher et al., J Proteome Res 5, 2270 (Sep, 2006).

48. M. Ohi, Y. Li, Y. Cheng, T. Walz, Biol Proced Online 6, 23 (2004).

49. S. J. Ludtke, P. R. Baldwin, W. Chiu, J Struct Biol 128, 82 (Dec 1, 1999).

50. M. van Heel, G. Harauz, E. V. Orlova, R. Schmidt, M. Schatz, J. Struct. Biol. 116, 17

(Jan-Feb, 1996).

51. D. N. Mastronarde, J Struct Biol 152, 36 (Oct, 2005).

52. J. A. Mindell, N. Grigorieff, J Struct Biol 142, 334 (Jun, 2003).

53. P. Dube, P. Tavares, R. Lurz, M. van Heel, EMBO J. 12, 1303 (Apr, 1993).

54. M. van Heel, J. Frank, Ultramicroscopy 6, 187 (1981).

55. M. van Heel, Ultramicroscopy 21, 111 (1987).

56. D. K. Clare et al., Structure 16, 528 (Apr, 2008).

57. C. V. Robinson, A. Sali, W. Baumeister, Nature 450, 973 (Dec 13, 2007).

58. D. Mourado, B. Kobe, N. E. Dixon, T. Huber, in Introduction to Protein Structure

Prediction, H. Rangwala, G. Karypis, Eds. (John Wiley & Sons, Inc., Hoboken,

NJ, USA, 2010), pp. 265-277.

59. F. Alber, F. Foerster, D. Korkin, M. Topf, A. Sali, Annual Review Of Biochemistry 77,

443 (Feb 01, 2008).

60. H. M. Berman et al., Nucleic Acids Res 28, 235 (Jan 1, 2000).

61. R. Das, D. Baker, Annual Review Of Biochemistry 77, 363 (Feb 01, 2008).

62. K. W. Kaufmann, G. H. Lemmon, S. L. Deluca, J. H. Sheehan, J. Meiler, Biochemistry

49, 2987 (Apr 13, 2010).

19  

63. A. Kahraman, L. Malmstrom, R. Aebersold, Bioinformatics 27, 2163 (Aug 1, 2011).

64. A. Zelter et al., Journal Of Proteome Research 9, 3583 (Feb 01, 2010).

65. D. Baker, Philos Trans R Soc Lond B Biol Sci 361, 459 (Mar 29, 2006).

66. C. A. Rohl, C. E. Strauss, K. M. Misura, D. Baker, Methods Enzymol 383, 66 (2004).

67. D. E. Kim, D. Chivian, D. Baker, Nucleic Acids Res 32, W526 (Jul 1, 2004).

68. D. T. Jones, J Mol Biol 292, 195 (Sep 17, 1999).

69. P. Rice, I. Longden, A. Bleasby, Trends Genet 16, 276 (Jun, 2000).

70. C. Wang, P. Bradley, D. Baker, J Mol Biol 373, 503 (Oct 19, 2007).

71. A. A. Canutescu, R. L. Dunbrack, Jr., Protein Sci 12, 963 (May, 2003).

72. A. Kahraman, R. J. Morris, R. A. Laskowski, A. D. Favia, J. M. Thornton, Proteins

78, 1120 (Apr, 2010).

73. A. Kahraman, R. J. Morris, R. A. Laskowski, J. M. Thornton, J Mol Biol 368, 283

(Apr 20, 2007).

74. J. Thompson, D. Baker, Proteins 79, 2380 (Aug, 2011).

75. S. Hubbard, J. Thornton, Naccess. (Computer Program, Department of Biochemistry

and Molecular Biology, University College London, 1993).

76. S. Bohn et al., Proc Natl Acad Sci U S A 107, 20992 (Dec 7, 2010).

77. R. Apweiler et al., Nucleic Acids Research 32, 115 (2004).

78. C. Chothia, A. M. Lesk, EMBO J 5, 823 (Apr, 1986).

79. D. Korkin et al., PLoS Comput Biol 2, e153 (Nov 10, 2006).

80. G. Kleywegt, T. Jones, CCP4/ESF-EACBM Newsletter on Protein Crystallography, 9

(Nov 30, 1994).

81. J. Soding, A. Biegert, A. N. Lupas, Nucleic Acids Res 33, W244 (Jul 1, 2005).

82. H. Hwang, T. Vreven, B. G. Pierce, J. H. Hung, Z. Weng, Proteins 78, 3104 (Nov 15,

2010).

83. A. Sali, T. L. Blundell, J Mol Biol 234, 779 (Dec 5, 1993).

84. J. Yang, S. M. Roe, T. D. Prickett, D. L. Brautigan, D. Barford, Biochemistry 46, 8807

(Jul 31, 2007).

85. M. Bantscheff, M. Schirle, G. Sweetman, J. Rick, B. Kuster, Anal Bioanal Chem 389,

1017 (Oct, 2007).

86. O. Llorca et al., Nature 402, 693 (Dec 9, 1999).

20  

Supplementary figures

Figure S1

Figure S1. Expression of affinity-tagged bait proteins in HEK293 cells.

ORFs were cloned in frame with a N-terminal His6-HA-StrepII-tag into the polylinker of the

pcDNA5/FRT/TO vector. Stable cell lines were generated in Flp-In T-Rex HEK293 cells and

protein expression was induced by adding tetracycline for 24 hours. Lysates of HEK293 cells

were separated by SDS-PAGE and proteins were detected by immuno-blotting using

antibodies raised against the HA peptide, the PP2A catalytic (C) subunits (PP2AA and

PP2AB) and PP2A regulatory subunits of the B subfamily (2ABA and 2ABG).

21  

Figure S2

22  

Figure S2. Titration of the protein to DSS concentration.

Protein complexes were purified using a tandem affinity protocol. Bait proteins were isolated

from the lysate through the Strep-tag and associated protein complexes were subsequently

recovered from the biotin eluate through the His6-tag (PD, pull-down; In, input; Sup,

supernatant; M, protein molecular weight marker). Immobilized proteins were incubated with

increasing concentrations of DSS and cross-linked proteins were separated by SDS-PAGE

and visualized by silver staining. The DSS concentration applied for the mass spectrometric

identification of cross-linked peptides is indicated in red. The titration experiments for protein

complexes associated with the bait proteins PP2AB (A), PP2AA (B), 2ABG (C), 2A5D (D),

2A5G (E), SGOL1 (F), FR1OP (G) and IGBP1 (H) are displayed.

Figure

e S3

23 

24 

25  

Figure S3. Fragment ion spectra of inter-protein cross-linked peptides identified on

PP2A complexes.

Protein complexes were cross-linked using isotopically labeled dissuccinimidyl suberate.

Cross-linked peptides were analyzed by LC-MS/MS and the positions of the linked lysine

residues were identified by the search engine xQuest (red label, cross-link ion; green label,

common ion does not carry the cross-linker) (chapters M3 and M5).

(A) PP2A trimeric complex: 2AAA(546)-PP2AA(74), 2AAA(34)-2A5D(500), PP2AA(41)-

2A5G(507). (B) IGBP1 in complex with PP2AA or PP4C: PP2AA(34)-IGBP1(166),

PP4C(31)-IGBP1(166). (C) PP2A trimer in complex with SGOL1: PP2AB(283)-SGOL1(35),

2A5G(28)-SGOL1(164. (D) 2ABG in complex with TRiC: TCPG(21)-2ABG(260),

2ABG(288)-TCPZ(10), 2ABG(263)-TCPG(21).

26  

Figure S4

27  

Figure S4. Evaluation of cross-link identifications on X-ray crystal structures and

comparative models.

The crystal structures of the trimeric 2AAA/2A5G/PP2AA (PDB entry 3FGA) and

2AAA/2ABA/PP2AA (PDB entry 3DW8) complex were used as templates for comparative

modeling of human paralogous forms of the PP2A holoenzyme using ROSETTA (chapter

M10.2.1). The arrangement of subunits was determined by structurally superimposing Cɑ

atoms of the comparative models on corresponding Cɑ atoms of the template structures. To

avoid redundancy, the paralogous subunits were combinatorially assembled as dimers. The

distances between cross-linked lysines were measured on the crystal structures and

comparative models of PP2A complexes specified by regulatory subunits of the B  (A) and B'

(B) subfamilies. (C) Determination of cross-link distances on a comparative model of a

human TRiC ring (tables S4 and S5). (A-C) The distance measurements were performed by

using Xwalk (63).

28  

Figure S5

29  

Figure S5. Cɑ-Cɑ distance distributions for intra- and inter-protein cross-links.

The distance measurements were performed on X-ray structures of PP2A trimeric complexes

and interactors and on comparative models of PP2A complexes and the TRiC chaperonin

complex (tables S4 and S5). The distances were determined by using Xwalk (63). (A)

Histograms of Euclidean distances spanned between Cɑ coordinates of cross-linked lysines on

trimeric PP2A complexes and a TRiC ring. The estimated maximum Euclidean distance

threshold of 30.0 Å is indicated (dotted line). (B) Histograms of SAS distances measured

between Cɑ coordinates of cross-linked lysines on trimeric PP2A complexes and a TRiC ring.

The estimated maximum SAS distance threshold of 34.0 Å is indicated. (C) Histograms

showing the SAS distances for all 287 intra-protein and 70 inter-protein cross-links for which

structural coordinates were available (tables S4 and S5). The median of the distance

distribution is indicated in red. (D) Statistics on inter- and intra-protein cross-link distances

identified on PP2A complexes, TRiC or all proteins and complexes of the PP2A network.

(E) Significance test results obtained by the Wilcoxon rank-sum test for the

distance distributions of intra-protein and inter-protein cross-links (Fig. 2C; fig. S5C and

tables S4 and S5). The significance level α < 0.01 indicated that inter- and intra-protein

distance distributions were significantly different.

30  

Figure S6

31  

Figure S6. Localization of the IGBP1 C-terminal domain in full-length structural models

using intra-protein cross-links.

(A) Five full-length models of IGBP1 conforming to at least 60 out of 65 intra-protein cross-

links with SAS distances ≤ 34.0 Å and a RMSD < 10.0 Å to the template structure 3QC1

(chapter M10.2.2). All models were superimposed on their N-terminal domain (M1-R221). In

all five models the C-terminus is positioned at the same location relative to the N-terminal

domain. We observed that the five selected models hold their C-terminal domain at a large

cleft at the N-terminus which is formed between the helices ɑ5 and ɑ6 and the loop-regions

connecting ɑ1 with ɑ2 and ɑ3 with ɑ4 (B). The models are rainbow colored from the N-

terminus (blue) to the C-terminus (red). N-terminal domain of IGBP1 with helices labeled

according to (23). (C-D) Selected full-length model of IGBP1_1 (chapters M10.2.3 and

M10.2.4) with the N-terminal domain colored in blue and the C-terminal domain ranging

from D222 to G339 colored in red. (C) Shortest paths for 18 intra-protein cross-links within

the C-terminal domain (light green) and 32 inter-domain cross-links between the N and C-

terminal domain (dark green). The surface representation was constructed on the protein

backbone and Cβ atoms. (D) Position of the IGBP1_1 C-terminal domain relative to its N-

terminus with the unresolved fold of the C-terminal domain indicated by a transparent cartoon

representation.

32  

Figure S7

33  

Figure S7. Predicted interfaces between IGBP1 and the catalytic subunits PP2AA or

PP4C using computational docking and seven or three inter-protein cross-links,

respectively.

(A) Docking calculations of IGBP1 and PP2AA driven by cross-link data. The IGBP1-

PP2AA docking models clustered in 237 groups. The models with the lowest ROSETTA score

of each group are shown in green. (B) The frequency of amino acids participating in the 237

predicted interfaces was assessed for both proteins (chapter M10.2.4). K163 of IGBP1 and

E37 of PP2AA were detected as the most frequent interface-residues at the relative

frequencies of 54% and 69%, respectively (table S11). The frequency analysis of IGBP1-

PP2AA TOP4 models (chapter M10.2.4) revealed the same amino acids with K163 of IGBP1

and E37 of PP2AA being the most frequent interface-residues at the relative frequency of

95%. (Fig. 3C and table S11). R155 and K158 of IGBP1 and E42 of PP2AA are in close

proximity to the most frequent interface-residues and were previously shown to be essential

for binding of IGBP1 to PP2AA (22, 84). (C-D) Docking calculations between IGBP1 and

PP4C resulted in 212 clusters, with R155 and E34 as the most frequent interface-residues,

respectively. E34 of PP4C corresponds to E37 of the homologous PP2A catalytic subunit

PP2AA (24). Cɑ coordinates of PP4C were superaligned with Cɑ coordinates of PP2AA

(PDB entry 3FGA) using the Kabsch algorithm as implemented in the CleftXplorer. (E) The

docking models with the lowest ROSETTA score within each of the TOP4 clusters of IGBP1-

PP4C (chapter M10.2.4) are shown in dark and light green. IGBP1 was found in two

predominant orientations to PP4C with one similar to IGBP1-PP2AA models (dark green)

(Fig. 3B). (F) K163 of IGBP1 and E34 of PP4C were identified as the most frequent

interface-residues in IGBP1-PP4C TOP4 docking models (table S11).

34  

Figure S8

Figure S8. Comparison of the best docking models for the IGBP1-PP2AA complex using

a docking procedure constrained by SAS or Euclidean distance restraints or lacking

restraints.

Selected models were aligned with the PP2AA subunit in the trimeric PP2A complex (PDB

entry 3FGA). (A) TOP4 models were selected by using a Xwalk SAS distance filter and

following the docking workflow described in chapter M10.2.3. (Fig. 3B). In total seven inter-

protein cross-links were used as distance restrains in the ROSETTA scoring function and as a

distance filter. The SAS distance measure facilitated the application of 10 intra-protein cross-

links and 10 mono-links to further constrain the docking calculations (chapter M10.1.3.4) (B)

Best models selected by a Euclidean distance filter using seven inter-protein cross-links and

following the docking procedure described in chapter M10.2.3. The lowest scoring models of

the TOP4 clusters obtained by Euclidean or SAS distance constrained docking revealed

similar IGBP1-PP2AA binding interfaces. (C) Ab initio unconstrained docking was performed

without any experimental distance information. Following the protocol described in chapter

M10.2.3 resulted in 10 clusters, whose lowest scoring representatives are shown. In all 10

cluster representatives, IGBP1 was located to a region of PP2AA which is opposite to the

IGBP1 binding sites determined by the cross-link distance constrained docking.

35  

Figure S9

Figure S9. Docking model of IGBP1 and PP2AA with the minimal average SAS

distance.

K163 of IGBP1 and E37 of PP2AA were found to be the most frequent interface-residues of

IGBP1-PP2AA docking models (Fig. 3C and fig. S7B). The model with the shortest average

SAS distance for all inter-protein cross-links displayed an Euclidean distance of 7.0 Å

between K163 and E37 positioning the two amino acids opposite to each other in close

proximity at the interface. The color code of the proteins corresponds to amino acid frequency

in fig. S7.

36  

Figure S10

Figure S10. Distribution of distances between the most frequent interface-residues in

IGBP1-PP2AA docking models.

The calculation of Euclidean Cα-Cα distances between K163 of IGBP1 and E37 of PP2AA

for the 37 TOP4 models (chapter M10.2.4.) revealed distances ranging from 6.7 to 16.6 Å.

37  

Figure S11

Figure S11. The binding sites of the PP2A scaffold subunit, 2AAA, and IGBP1 on the

catalytic subunit, PP2AA, show a minor overlap.

The interface between IGBP1 and PP2AA (red surface patches) and the interface between

2AAA and PP2AA (green surface patches) share in total three amino acids (black surface

region). The IGBP1-PP2AA interface corresponds to the interface shown in Fig. 3C. Only

residues having an interface frequency of above 50% were selected as potentially shared

amino acids. The interface of 2AAA-PP2AA was calculated from the 2A5G/2AAA/PP2AA

complex (PDB entry 3FGA) with Naccess. E37 of PP2AA was identified in 95% of the

predicted IGBP1-PP2A interfaces (Fig. 3C and table S11). E42 of PP2AA was detected at a

frequency of 32% and was previously shown to be essential for binding of PP2AA to IGBP1

(22).

Figure

e S12

38 

39  

Figure S12. Determination of the subunit stoichiometries of 2ABG associated protein

complexes by label-free quantification.

(A) Protein complexes co-purifying with 2ABG were analyzed by mass spectrometry. The

protein abundances were determined by label-free quantification. Protein abundances were

calculated from the sum of the precursor intensities of all proteotypic peptides. To account for

differences in replicate experiments, protein abundances were normalized to the abundance of

the bait protein. To calculate the subunit stoichiometry, protein abundances were further

normalized to the respective molecular weights of the proteins. The relative abundances of

proteins co-purifying with 2ABG suggest that 2ABG forms stoichiometric complexes with the

PP2A catalytic and scaffold subunits and with the TRiC subunits. (B) Label-free

quantification (85) of proteins in complex with 2ABG in three replicate experiments (Exp,

replicate experiment).

40  

Figure S13

Figure S13. Localization of 2ABG in the inner cavity at the equatorial plane of TRiC

using 19 inter-protein cross-links.

By minimizing the distances of inter-protein cross-links detected between 2ABG (black

protein) and the C- and N-terminal tails of six TRiC subunits (differently colored), 2ABG was

located at the equatorial plane in the inner cavity of TRiC. Red lines indicate cross-links

between TRiC subunits and β-sheets of the predicted WD40 propeller of 2ABG, while pink

lines indicate cross-links between TRiC subunits and loop regions of 2ABG. The four cross-

links to β-sheets were applied to position 2ABG in the inner cavity of TRiC (table S12)

(chapter M10.2.5). The Cɑ atoms of cross-linked lysine residues are shown as spheres and are

labeled according to their residue numbers. The single letters suffixed to the residue numbers

of cross-linked TRiC residues correspond to the last letters of their UniProt subunit names

(Fig. 4A). Protein structures were obtained by comparative modeling (chapters M10.1.3.2 and

M10.2.1).

41  

Figure S14

Figure S14. 2D image analysis of TRiC conformations by electron microscopy.

The average images show TRiC in half-open and open conformations. (A, B) Cryo-EM

average images of the cross-linked TRiC complex. (C, D) Average images from negatively

stained cross-linked TRiC complex. (E, F) Negative stain EM images from TRiC complex not

subjected to cross-linking. Scale bar 10 nm. Representative top views (A, C, E) and side

views (B, D ,F) are shown. Density inside the TRiC cavity (arrow) is attributed to a bound

substrate (86).

42  

Supplementary Tables

Table S1. Annotation of proteins in the PP2A network.

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q15172 2A5A Serine/threonine-protein

phosphatase 2A 56 kDa regulatory subunit alpha isoform (PP2A B subunit isoform B'-alpha) (PP2A B subunit isoform B56-alpha) (PP2A B subunit isoform PR61-alpha) (PR61alpha) (PP2A B subunit isoform R5-alpha)

PPP2R5A chromosome, centromeric region; cytoplasm; kinase binding; negative regulation of establishment of protein localization in plasma membrane; negative regulation of lipid kinase activity; nucleus; positive regulation of protein dephosphorylation; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

486

Q15173 2A5B Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform (PP2A B subunit isoform B'-beta) (PP2A B subunit isoform B56-beta) (PP2A B subunit isoform PR61-beta) (PP2A B subunit isoform R5-beta)

PPP2R5B activation of signaling protein activity involved in unfolded protein response; cytosol; protein binding; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity

497

Q14738 2A5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PP2A B subunit isoform B'-delta) (PP2A B subunit isoform B56-delta) (PP2A B subunit isoform PR61-delta) (PP2A B subunit isoform R5-delta)

PPP2R5D cytoplasm; nervous system development; nucleus; protein binding; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

602

Q16537 2A5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform (PP2A B subunit isoform B'-epsilon) (PP2A B subunit isoform B56-epsilon) (PP2A B subunit isoform PR61-epsilon) (PP2A B subunit isoform R5-epsilon)

PPP2R5E cytoplasm; intracellular membrane-bounded organelle; protein binding; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

467

Q13362 2A5G Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (PP2A B subunit isoform B'-gamma) (PP2A B subunit isoform B56-gamma) (PP2A B subunit isoform PR61-gamma) (PP2A B subunit isoform R5-gamma) (Renal carcinoma antigen NY-REN-29)

PPP2R5C KIAA0044

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis; chromosome, centromeric region; negative regulation of cell proliferation; nucleus; proteasomal ubiquitin-dependent protein catabolic process; protein binding; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

524

43  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) P30153 2AAA Serine/threonine-protein

phosphatase 2A 65 kDa regulatory subunit A alpha isoform (Medium tumor antigen-associated 61 kDa protein) (PP2A subunit A isoform PR65-alpha) (PP2A subunit A isoform R1-alpha)

PPP2R1A G2/M transition of mitotic cell cycle; RNA splicing; antigen binding; ceramide metabolic process; chromosome segregation; chromosome, centromeric region; cytosol; fibroblast growth factor receptor signaling pathway; inactivation of MAPK activity; induction of apoptosis; membrane; microtubule cytoskeleton; mitochondrion; negative regulation of cell growth; negative regulation of tyrosine phosphorylation of Stat3 protein; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; nucleus; protein complex assembly; protein heterodimerization activity; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; regulation of DNA replication; regulation of Wnt receptor signaling pathway; regulation of cell adhesion; regulation of cell differentiation; regulation of transcription, DNA-dependent; second-messenger-mediated signaling; soluble fraction

589

P30154 2AAB Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A subunit A isoform PR65-beta) (PP2A subunit A isoform R1-beta)

PPP2R1B positive regulation of extrinsic apoptotic signaling pathway in absence of ligand; protein binding

601

P63151 2ABA Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A subunit B isoform B55-alpha) (PP2A subunit B isoform PR55-alpha) (PP2A subunit B isoform R2-alpha) (PP2A subunit B isoform alpha)

PPP2R2A cytosol; gene expression; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; protein binding; protein dephosphorylation; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; protein serine/threonine phosphatase activity; signal transduction

447

Q66LE6 2ABD Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform (PP2A subunit B isoform B55-delta) (PP2A subunit B isoform PR55-delta) (PP2A subunit B isoform R2-delta) (PP2A subunit B isoform delta)

PPP2R2D KIAA1541

cell division; exit from mitosis; mitosis; protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

453

44  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q9Y2T4 2ABG Serine/threonine-protein

phosphatase 2A 55 kDa regulatory subunit B gamma isoform (IMYPNO1) (PP2A subunit B isoform B55-gamma) (PP2A subunit B isoform PR55-gamma) (PP2A subunit B isoform R2-gamma) (PP2A subunit B isoform gamma)

PPP2R2C protein phosphatase type 2A complex; protein phosphatase type 2A regulator activity; signal transduction

447

Q86XL3 ANKL2 Ankyrin repeat and LEM domain-containing protein 2

ANKLE2 KIAA0692

cytoplasm; integral to membrane; nuclear envelope

938

Q16204 CCDC6 Coiled-coil domain-containing protein 6 (Papillary thyroid carcinoma-encoded protein) (Protein H4)

CCDC6 D10S170 TST1

SH3 domain binding; cytoplasm; cytoskeleton; structural constituent of cytoskeleton

474

P51959 CCNG1 Cyclin-G1 (Cyclin-G) CCNG1 CCNG CYCG1

cell division; mitosis; nucleus; regulation of cyclin-dependent protein kinase activity

295

Q69YH5 CDCA2 Cell division cycle-associated protein 2 (Recruits PP1 onto mitotic chromatin at anaphase protein) (Repo-Man)

CDCA2 cell division; cytoplasm; mitosis; nucleus 1023

Q9BXL8 CDCA4 Cell division cycle-associated protein 4 (Hematopoietic progenitor protein)

CDCA4 HEPP nucleus 241

Q5VT06 CE350 Centrosome-associated protein 350 (Cep350) (Centrosome-associated protein of 350 kDa)

CEP350 CAP350 KIAA0480 GM133

centrosome; nucleus; spindle 3117

Q5TF21 CF174 Uncharacterized protein C6orf174

C6orf174 integral to membrane 947

Q96N11 CG026 Uncharacterized protein C7orf26

C7orf26 449

Q96SY0 CO044 UPF0464 protein C15orf44 C15orf44 518

Q9P2B4 CT2NL CTTNBP2 N-terminal-like protein

CTTNBP2NL KIAA1433

actin cytoskeleton; protein binding 639

Q8WZ74 CTTB2 Cortactin-binding protein 2 (CortBP2)

CTTNBP2 C7orf8 CORTBP2 KIAA1758

1663

Q9NTK1 DEPP Protein DEPP (Decidual protein induced by progesterone) (Fasting-induced gene protein) (FIG)

DEPP C10orf10 FIG mitochondrion 212

45  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) O60610 DIAP1 Protein diaphanous homolog

1 (Diaphanous-related formin-1) (DRF1)

DIAPH1 DIAP1 actin binding; cellular response to histamine; cytoplasm; ion channel binding; mitotic spindle; protein localization to microtubule; receptor binding; regulation of cell shape; regulation of microtubule-based process; regulation of release of sequestered calcium ion into cytosol; ruffle membrane; sensory perception of sound

1272

P63167 DYL1 Dynein light chain 1, cytoplasmic (8 kDa dynein light chain) (DLC8) (Dynein light chain LC8-type 1) (Protein inhibitor of neuronal nitric oxide synthase) (PIN)

DYNLL1 DLC1 DNCL1 DNCLC1

HDLC1

G2/M transition of mitotic cell cycle; actin cytoskeleton organization; activation of pro-apoptotic gene products; anatomical structure morphogenesis; centrosome; cytoplasmic dynein complex; cytosol; female gamete generation; induction of apoptosis by intracellular signals; interspecies interaction between organisms; microtubule; microtubule-based process; mitochondrion; motor activity; negative regulation of phosphorylation; nucleus; plasma membrane; protein binding; regulation of transcription, DNA-dependent; transcription, DNA-dependent; transport

89

Q96FJ2 DYL2 Dynein light chain 2, cytoplasmic (8 kDa dynein light chain b) (DLC8b) (Dynein light chain LC8-type 2)

DYNLL2 DLC2 activation of pro-apoptotic gene products; centrosome; cytosol; dynein complex; induction of apoptosis by intracellular signals; microtubule; microtubule-based process; motor activity; myosin complex; plasma membrane; transport

89

Q9BQ95 ECSIT Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial (Protein SITPEC)

ECSIT innate immune response; mitochondrion; nucleus; oxidoreductase activity, acting on NADH or NADPH; protein binding; regulation of oxidoreductase activity

431

Q14674 ESPL1 Separin (EC 3.4.22.49) (Caspase-like protein ESPL1) (Extra spindle poles-like 1 protein) (Separase)

ESPL1 ESP1 KIAA0165

apoptotic process; centrosome; cysteine-type peptidase activity; cytokinesis; establishment of mitotic spindle localization; mitotic sister chromatid segregation; negative regulation of sister chromatid cohesion; nucleus; positive regulation of mitotic metaphase/anaphase transition; protein binding; proteolysis

2120

Q96E09 F122A Protein FAM122A FAM122A C9orf42 287

Q96C01 F136A Protein FAM136A FAM136A mitochondrion 138

O94988 FA13A Protein FAM13A FAM13A FAM13A1 KIAA0914

GTPase activator activity; cytosol; regulation of small GTPase mediated signal transduction; small GTPase mediated signal transduction

1023

Q5VSL9 FA40A Protein FAM40A FAM40A KIAA1761

cortical actin cytoskeleton organization; cytoplasm; nucleus; protein binding; regulation of cell morphogenesis

837

Q9ULQ0 FA40B Protein FAM40B FAM40B KIAA1170

cell migration; cytoplasm; cytoskeleton organization; regulation of cell shape

834

46  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q6P3S6 FBX42 F-box only protein 42 (Just

one F-box and Kelch domain-containing protein)

FBXO42 FBX42 JFK KIAA1332

717

O95684 FR1OP FGFR1 oncogene partner FGFR1OP FOP G2/M transition of mitotic cell cycle; centrosome; cytosol; microtubule anchoring; nucleus; perinuclear region of cytoplasm; positive regulation of cell growth; positive regulation of cell migration; positive regulation of cell proliferation; protein homodimerization activity; protein kinase binding; protein tyrosine kinase inhibitor activity

399

O94927 HAUS5 HAUS augmin-like complex subunit 5

HAUS5 KIAA0841 HAUS complex; cell division; centrosome; centrosome organization; microtubule; mitosis; spindle; spindle assembly

633

P22830 HEMH Ferrochelatase, mitochondrial (EC 4.99.1.1) (Heme synthase) (Protoheme ferro-lyase)

FECH 2 iron, 2 sulfur cluster binding; ferrochelatase activity; ferrous iron binding; generation of precursor metabolites and energy; heme biosynthetic process; mitochondrial inner membrane; mitochondrial matrix; protein binding; protoporphyrinogen IX metabolic process; response to light stimulus; small molecule metabolic process

423

P78318 IGBP1 Immunoglobulin-binding protein 1 (B-cell signal transduction molecule alpha 4) (Protein alpha-4) (CD79a-binding protein 1) (Renal carcinoma antigen NY-REN-16)

IGBP1 IBP1 B cell activation; cytoplasm; negative regulation of cysteine-type endopeptidase activity involved in apoptotic process; negative regulation of stress-activated MAPK cascade; negative regulation of transcription from RNA polymerase II promoter; protein phosphatase type 2A regulator activity; regulation of microtubule-based movement; response to interleukin-1; response to tumor necrosis factor; signal transduction

339

Q9NVR2 INT10 Integrator complex subunit 10 (Int10)

INTS10 C8orf35 cytoplasm; integrator complex; snRNA processing

710

Q5TA45 INT11 Integrator complex subunit 11 (Int11) (EC 3.1.27.-) (Cleavage and polyadenylation-specific factor 3-like protein) (CPSF3-like protein) (Protein related to CPSF subunits of 68 kDa) (RC-68)

CPSF3L INTS11 RC68

cytoplasm; hydrolase activity; nucleus 600

Q96CB8 INT12 Integrator complex subunit 12 (Int12) (PHD finger protein 22)

INTS12 PHF22 SBBI22

integrator complex; protein binding; snRNA processing; zinc ion binding

462

Q8N201 INT1 Integrator complex subunit 1 (Int1)

INTS1 KIAA1440 UNQ1821/PRO3434

integral to membrane; integrator complex; nuclear membrane

2190

47  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q9H0H0 INT2 Integrator complex subunit 2

(Int2) INTS2 KIAA1287 integral to membrane; integrator complex;

nuclear membrane; protein binding; snRNA processing

1204

Q68E01 INT3 Integrator complex subunit 3 (Int3) (SOSS complex subunit A) (Sensor of single-strand DNA complex subunit A) (SOSS-A) (Sensor of ssDNA subunit A)

INTS3 C1orf193 C1orf60

DNA repair; G2/M transition checkpoint; SOSS complex; integrator complex; protein binding; response to ionizing radiation; snRNA processing

1043

Q96HW7 INT4 Integrator complex subunit 4 (Int4)

INTS4 MSTP093 integrator complex; protein binding; snRNA processing

963

Q6P9B9 INT5 Integrator complex subunit 5 (Int5)

INTS5 KIAA1698 integral to membrane; integrator complex; protein binding; snRNA processing

1019

Q9UL03 INT6 Integrator complex subunit 6 (Int6) (DBI-1) (Protein DDX26) (Protein deleted in cancer 1) (DICE1)

INTS6 DBI1 DDX26 DDX26A

actin cytoskeleton; integrator complex; protein binding; snRNA processing; transmembrane signaling receptor activity

887

Q9NVH2 INT7 Integrator complex subunit 7 (Int7)

INTS7 C1orf73 DNA damage checkpoint; cellular response to ionizing radiation; chromosome; integrator complex; protein binding; snRNA processing

962

Q75QN2 INT8 Integrator complex subunit 8 (Int8) (Protein kaonashi-1)

INTS8 C8orf52 integrator complex; protein binding; snRNA processing

995

Q9NV88 INT9 Integrator complex subunit 9 (Int9) (Protein related to CPSF subunits of 74 kDa) (RC-74)

INTS9 RC74 integrator complex; protein binding; snRNA processing

658

O94964 K0889 Uncharacterized protein KIAA0889

KIAA0889 C20orf117

1423

Q13557 KCC2D Calcium/calmodulin-dependent protein kinase type II subunit delta (CaM kinase II subunit delta) (CaMK-II subunit delta) (EC 2.7.11.17)

CAMK2D CAMKD ATP binding; calcium- and calmodulin-dependent protein kinase complex; calmodulin binding; calmodulin-dependent protein kinase activity; cytosol; endocytic vesicle membrane; interferon-gamma-mediated signaling pathway; nucleoplasm; positive regulation of cardiac muscle hypertrophy; regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion; regulation of cell growth; regulation of ryanodine-sensitive calcium-release channel activity; sarcoplasmic reticulum membrane; synaptic transmission

499

48  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q13555 KCC2G Calcium/calmodulin-

dependent protein kinase type II subunit gamma (CaM kinase II subunit gamma) (CaMK-II subunit gamma) (EC 2.7.11.17)

CAMK2G CAMK CAMK-II CAMKG

ATP binding; calcium- and calmodulin-dependent protein kinase complex; calcium-dependent protein serine/threonine phosphatase activity; calmodulin binding; calmodulin-dependent protein kinase activity; cell differentiation; cytosol; endocytic vesicle membrane; insulin secretion; interferon-gamma-mediated signaling pathway; nervous system development; nucleoplasm; plasma membrane; regulation of calcium ion transport; regulation of skeletal muscle adaptation; sarcoplasmic reticulum membrane; synaptic transmission

558

Q9NVM9 ASUN Protein asunder homolog (Cell cycle regulator Mat89Bb homolog) (Sarcoma antigen NY-SAR-95)

Asun C12orf11 cell division; cytoplasm; mitosis; nucleus; protein binding; regulation of fertilization; regulation of mitotic cell cycle; sperm motility

706

Q13136 LIPA1 Liprin-alpha-1 (LAR-interacting protein 1) (LIP-1) (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-1) (PTPRF-interacting protein alpha-1)

PPFIA1 LIP1 cell-matrix adhesion; cytoplasm; protein binding; signal transducer activity

1202

O75334 LIPA2 Liprin-alpha-2 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2) (PTPRF-interacting protein alpha-2)

PPFIA2 cell surface; cell-matrix adhesion; cytoplasm; protein binding

1257

O75145 LIPA3 Liprin-alpha-3 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3) (PTPRF-interacting protein alpha-3)

PPFIA3 KIAA0654 cell surface; cytoplasm; protein binding 1194

O95819 M4K4 Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) (HPK/GCK-like kinase HGK) (MAPK/ERK kinase kinase kinase 4) (MEK kinase kinase 4) (MEKKK 4) (Nck-interacting kinase)

MAP4K4 HGK KIAA0687 NIK

ATP binding; cytoplasm; intracellular protein kinase cascade; protein binding; protein serine/threonine kinase activity; regulation of JNK cascade; response to stress; small GTPase regulator activity

1239

Q9P289 MST4 Serine/threonine-protein kinase MST4 (EC 2.7.11.1) (Mammalian STE20-like protein kinase 4) (MST-4) (Mst3 and SOK1-related kinase) (STE20-like kinase MST4) (Serine/threonine-protein kinase MASK)

MST4 MASK ATP binding; Golgi membrane; cellular component disassembly involved in apoptosis; cytosol; identical protein binding; magnesium ion binding; protein serine/threonine kinase activity; regulation of apoptotic process

416

49  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q969Q6 P2R3C Serine/threonine-protein

phosphatase 2A regulatory subunit B'' subunit gamma (Protein phosphatase subunit G5PR) (Rhabdomyosarcoma antigen MU-RMS-40.6A/6C)

PPP2R3C C14orf10 G5PR

calcium ion binding; centrosome; nucleus 453

Q6IN85 P4R3A Serine/threonine-protein phosphatase 4 regulatory subunit 3A (SMEK homolog 1)

SMEK1 KIAA2010 PP4R3A PPP4R3A

MSTP033

binding; microtubule organizing center; nucleus

833

Q5MIZ7 P4R3B Serine/threonine-protein phosphatase 4 regulatory subunit 3B (SMEK homolog 2)

SMEK2 KIAA1387 PP4R3B PPP4R3B

binding; microtubule organizing center; nucleus

849

Q9BUL8 PDC10 Programmed cell death protein 10 (Cerebral cavernous malformations 3 protein) (TF-1 cell apoptosis-related protein 15)

PDCD10 CCM3 TFAR15

Golgi membrane; angiogenesis; apoptotic process; cytosol; negative regulation of apoptotic process; plasma membrane; positive regulation of MAP kinase activity; positive regulation of cell proliferation; protein N-terminus binding; protein homodimerization activity

212

Q9Y3A3 PHOCN MOB-like protein phocein (2C4D) (Class II mMOB1) (Mob1 homolog 3) (Mob3) (Mps one binder kinase activator-like 3) (Preimplantation protein 3)

MOB4 MOB3 MOBKL3 PHOCN

PREI3 CGI-95

Golgi cisterna membrane; metal ion binding; perinuclear region of cytoplasm; protein binding; transport

225

P67775 PP2AA Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (PP2A-alpha) (EC 3.1.3.16) (Replication protein C) (RP-C)

PPP2CA RNA splicing; ceramide metabolic process; chromosome, centromeric region; cytosol; fibroblast growth factor receptor signaling pathway; inactivation of MAPK activity; induction of apoptosis; meiosis; metal ion binding; mitochondrion; negative regulation of cell growth; negative regulation of epithelial to mesenchymal transition; negative regulation of tyrosine phosphorylation of Stat3 protein; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; nucleus; phosphoprotein phosphatase activity; positive regulation of protein serine/threonine kinase activity; protein dephosphorylation; protein phosphatase type 2A complex; regulation of DNA replication; regulation of Wnt receptor signaling pathway; regulation of cell adhesion; regulation of transcription, DNA-dependent; second-messenger-mediated signaling; soluble fraction; spindle pole

309

50  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) P62714 PP2AB Serine/threonine-protein

phosphatase 2A catalytic subunit beta isoform (PP2A-beta) (EC 3.1.3.16)

PPP2CB chromosome, centromeric region; cytosol; fibroblast growth factor receptor signaling pathway; metal ion binding; nucleus; protein dephosphorylation; protein phosphatase type 2A complex; spindle pole

309

P60510 PP4C Serine/threonine-protein phosphatase 4 catalytic subunit (PP4C) (Pp4) (EC 3.1.3.16) (Protein phosphatase X) (PP-X)

PPP4C PPP4 PPX NF-kappaB-inducing kinase activity; centrosome; metal ion binding; microtubule cytoskeleton organization; nucleus; protein binding; protein serine/threonine phosphatase activity; regulation of double-strand break repair via homologous recombination

307

Q8TF05 PP4R1 Serine/threonine-protein phosphatase 4 regulatory subunit 1

PPP4R1 MEG1 PP4R1

protein binding; protein phosphatase 4 complex; protein phosphatase type 4 regulator activity; protein phosphorylation; signal transduction

950

Q9NY27 PP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2

PPP4R2 SBBI57 RNA splicing; centrosome; mRNA processing; nucleus; protein binding, bridging; protein modification process; protein phosphatase 4 complex; protein phosphatase type 4 regulator activity; regulation of double-strand break repair via homologous recombination

417

Q6NUP7 PP4R4 Serine/threonine-protein phosphatase 4 regulatory subunit 4

PPP4R4 KIAA1622 PP4R4

cytoplasm; protein binding; protein serine/threonine phosphatase complex

873

Q9Y570 PPME1 Protein phosphatase methylesterase 1 (PME-1) (EC 3.1.1.89)

PPME1 PME1 PP2593 PRO0750

carboxylesterase activity; protein C-terminal methylesterase activity; protein demethylation; protein phosphatase 2A binding; protein phosphatase inhibitor activity; protein phosphatase type 2A regulator activity

386

O00743 PPP6 Serine/threonine-protein phosphatase 6 catalytic subunit (PP6C) (EC 3.1.3.16)

PPP6C PPP6 G1/S transition of mitotic cell cycle; cytosol; metal ion binding; protein binding; protein dephosphorylation; protein serine/threonine phosphatase activity

305

Q5THK1 PR14L Protein PRR14L (Proline rich 14-like protein)

PRR14L C22orf30 2151

Q9BWN1 PRR14 Proline-rich protein 14 PRR14 585

P24928 RPB1 DNA-directed RNA polymerase II subunit RPB1 (RNA polymerase II subunit B1) (EC 2.7.7.6) (DNA-directed RNA polymerase II subunit A) (DNA-directed RNA polymerase III largest subunit) (RNA-directed RNA polymerase II subunit RPB1) (EC 2.7.7.48)

POLR2A POLR2 DNA binding; DNA-directed RNA polymerase II, core complex; DNA-directed RNA polymerase activity; RNA-directed RNA polymerase activity; mRNA capping; metal ion binding; nuclear mRNA splicing, via spliceosome; positive regulation of viral transcription; protein phosphorylation; regulation of transcription, DNA-dependent; transcription elongation from RNA polymerase II promoter; transcription initiation from RNA polymerase II promoter; transcription-coupled nucleotide-excision repair; ubiquitin protein ligase binding; viral reproduction

1970

51  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) P30876 RPB2 DNA-directed RNA

polymerase II subunit RPB2 (EC 2.7.7.6) (DNA-directed RNA polymerase II 140 kDa polypeptide) (DNA-directed RNA polymerase II subunit B) (RNA polymerase II subunit 2) (RNA polymerase II subunit B2)

POLR2B DNA binding; DNA-directed RNA polymerase II, core complex; DNA-directed RNA polymerase activity; mRNA capping; metal ion binding; nuclear mRNA splicing, via spliceosome; positive regulation of viral transcription; protein binding; protein phosphorylation; ribonucleoside binding; transcription elongation from RNA polymerase II promoter; transcription initiation from RNA polymerase II promoter; transcription-coupled nucleotide-excision repair; viral reproduction

1174

P19387 RPB3 DNA-directed RNA polymerase II subunit RPB3 (RNA polymerase II subunit 3) (RNA polymerase II subunit B3) (DNA-directed RNA polymerase II 33 kDa polypeptide) (RPB33) (DNA-directed RNA polymerase II subunit C) (RPB31)

POLR2C A-152E5.7 DNA binding; DNA-directed RNA polymerase II, core complex; DNA-directed RNA polymerase activity; mRNA capping; microtubule cytoskeleton; nuclear mRNA splicing, via spliceosome; positive regulation of viral transcription; protein dimerization activity; protein phosphorylation; transcription elongation from RNA polymerase II promoter; transcription initiation from RNA polymerase II promoter; transcription-coupled nucleotide-excision repair; viral reproduction

275

Q01105 SET Protein SET (HLA-DR-associated protein II) (Inhibitor of granzyme A-activated DNase) (IGAAD) (PHAPII) (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template-activating factor I) (TAF-I)

SET DNA replication; cytosol; endoplasmic reticulum; gene expression; histone binding; mRNA metabolic process; negative regulation of histone acetylation; negative regulation of neuron apoptosis; negative regulation of transcription, DNA-dependent; nucleocytoplasmic transport; nucleoplasm; nucleosome assembly; nucleosome disassembly; perinuclear region of cytoplasm; protein complex; protein phosphatase inhibitor activity; protein phosphatase type 2A regulator activity

290

Q5FBB7 SGOL1 Shugoshin-like 1 (hSgo1) (Serologically defined breast cancer antigen NY-BR-85)

SGOL1 SGO1 attachment of spindle microtubules to kinetochore; cell division; centriole-centriole cohesion; centrosome; condensed chromosome kinetochore; cytosol; meiotic chromosome segregation; mitotic cohesin complex; mitotic prometaphase; protein binding; spindle pole

561

Q562F6 SGOL2 Shugoshin-like 2 (Shugoshin-2) (Sgo2) (Tripin)

SGOL2 cell division; condensed chromosome kinetochore; cytosol; mitotic cohesin complex; mitotic prometaphase; protein binding

1265

Q9BRV8 SIKE1 Suppressor of IKBKE 1 (Suppressor of IKK-epsilon)

SIKE1 SIKE cytosol; focal adhesion; innate immune response; intracellular membrane-bounded organelle; protein binding

207

Q9NRY2 SOSSC SOSS complex subunit C (Sensor of single-strand DNA complex subunit C) (Sensor of ssDNA subunit C) (SOSS-C) (Single-stranded DNA-binding protein-interacting protein 1) (SSB-interacting protein 1) (hSSBIP1)

SSBIP1 C9orf80 HSPC043 HSPC291

DNA repair; SOSS complex; protein binding; response to ionizing radiation

104

52  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) Q9Y6E0 STK24 Serine/threonine-protein

kinase 24 (EC 2.7.11.1) (Mammalian STE20-like protein kinase 3) (MST-3) (STE20-like kinase MST3) [Cleaved into: Serine/threonine-protein kinase 24 36 kDa subunit (Mammalian STE20-like protein kinase 3 N-terminal) (MST3/N); Serine/threonine-protein kinase 24 12 kDa subunit (Mammalian STE20-like protein kinase 3 C-terminal) (MST3/C)]

STK24 MST3 STK3 ATP binding; cellular component disassembly involved in apoptosis; cytosol; induction of apoptosis by oxidative stress; membrane; metal ion binding; negative regulation of cell migration; nucleoplasm; protein autophosphorylation; protein binding; protein serine/threonine kinase activity; regulation of axon regeneration; signal transduction

443

Q13033 STRN3 Striatin-3 (Cell cycle autoantigen SG2NA) (S/G2 antigen) (PP2A regulatory subunit B''')

STRN3 GS2NA SG2NA

Golgi apparatus; armadillo repeat domain binding; calmodulin binding; cytoplasm; dendrite; negative regulation of intracellular estrogen receptor signaling pathway; negative regulation of transcription from RNA polymerase II promoter; neuronal cell body; nucleoplasm; nucleus; plasma membrane; positive regulation of transcription from RNA polymerase II promoter; protein complex; protein complex binding; protein phosphatase 2A binding; response to estradiol stimulus; sequence-specific DNA binding transcription factor activity

797

Q9NRL3 STRN4 Striatin-4 (Zinedin) (PP2A regulatory subunit B''')

STRN4 ZIN armadillo repeat domain binding; calmodulin binding; cytoplasm; membrane; protein complex binding; protein phosphatase 2A binding

753

O43815 STRN Striatin (PP2A regulatory subunit B''')

STRN Wnt receptor signaling pathway; armadillo repeat domain binding; calmodulin binding; cytoplasm; dendrite development; estrogen receptor binding; locomotory behavior; negative regulation of cell proliferation; neuronal cell body; postsynaptic density; postsynaptic membrane; protein complex binding; protein phosphatase 2A binding; tight junction; tight junction assembly

780

P17987 TCPA T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)

TCP1 CCT1 CCTA 'de novo' posttranslational protein folding; ATP binding; Golgi apparatus; cell junction; plasma membrane; tubulin complex assembly; unfolded protein binding

556

P78371 TCPB T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)

CCT2 99D8.1 CCTB

'de novo' posttranslational protein folding; ATP binding; chaperone-mediated protein complex assembly; nucleus; unfolded protein binding

535

P50991 TCPD T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta) (Stimulator of TAR RNA-binding)

CCT4 CCTD SRB 'de novo' posttranslational protein folding; ATP binding; centrosome; melanosome; nucleus; unfolded protein binding

539

P48643 TCPE T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)

CCT5 CCTE KIAA0098

'de novo' posttranslational protein folding; ATP binding; centrosome; nucleolus; response to virus; unfolded protein binding

541

53  

UniProt entry

UniProt name

Protein names Gene names Gene ontology (GO) Length

(aa) P49368 TCPG T-complex protein 1 subunit

gamma (TCP-1-gamma) (CCT-gamma) (hTRiC5)

CCT3 CCTG TRIC5 'de novo' posttranslational protein folding; ATP binding; cytoskeleton; cytosol; plasma membrane; unfolded protein binding

545

Q99832 TCPH T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta) (HIV-1 Nef-interacting protein)

CCT7 CCTH NIP7-1

'de novo' posttranslational protein folding; ATP binding; unfolded protein binding

543

P50990 TCPQ T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta) (Renal carcinoma antigen NY-REN-15)

CCT8 C21orf112 CCTQ KIAA0002

'de novo' posttranslational protein folding; ATP binding; ATPase activity, coupled; aggresome; centrosome; cytosol; intermediate filament cytoskeleton; unfolded protein binding

548

P40227 TCPZ T-complex protein 1 subunit zeta (TCP-1-zeta) (Acute morphine dependence-related protein 2) (CCT-zeta-1) (HTR3) (Tcp20)

CCT6A CCT6 CCTZ

'de novo' posttranslational protein folding; ATP binding; unfolded protein binding

531

Q9Y4R8 TELO2 Telomere length regulation protein TEL2 homolog (Protein clk-2 homolog) (hCLK2)

TELO2 KIAA0683 chromosome, telomeric region; cytoplasm; membrane; nucleus; protein binding

837

54  

Table S2. Summary of bait proteins used for affinity-purification and cross-linking

experiments.

The cDNAs of bait proteins were retrieved from the human orfeome library (horfeome v5.1)

or amplified from the MegaMan Human Transcriptome library. Protein complexes interacting

with the bait proteins were purified via their N-terminal His6-HA-StrepII-tag and analyzed by

mass spectrometry prior or subsequent to cross-linking with DSS. (horfeome, human orfeome

library identifier (-, MegaMan); aa, amino acid number of bait protein; XL, replicate cross-

linking experiments per bait protein; AP, replicate affinity-purification experiments per bait

protein)

horfeome UniProt

entry Uniprot

name Gene

names Protein names

Length (aa)

XL AP

2961 Q14738 2A5D PPP2R5D PP2A B subunit isoform B'-delta, -B56-delta, -PR61-delta, -R5-delta

602 2 3

- Q16537 2A5E PPP2R5E PP2A B subunit isoform B'-epsilon, -

B56-epsilon, -PR61-epsilon, -R5-epsilon

467 2 3

7603 Q13362 2A5G PPP2R5C PP2A B subunit isoform B'-gamma, -

B56-gamma, -PR61-gamma, -R5-gamma

524 2 3

13596 P63151 2ABA PPP2R2A PP2A subunit B isoform B55-alpha, -

PR55-alpha, -R2-alpha, -alpha 447 2 3

1776 Q9Y2T4 2ABG PPP2R2C PP2A subunit B isoform B55-gamma, -

PR55-gamma, -R2-gamma, -gamma 447 4 5

1551 P30154 2AAB PPP2R1B PP2A subunit A isoform PR65-beta, -

R1-beta 601 2 4

4071 P67775 PP2AA PPP2CA PP2A catalytic subunit alpha isoform,

PP2A-alpha 309 2 3

1089 P62714 PP2AB PPP2CB PP2A catalytic subunit beta isoform,

PP2A-beta 309 5 5

7929 P60510 PP4C PPP4C, PPP4 PP4 catalytic subunit, PP4C 307 2 3

290 Q9P2B4 CT2NL CTTNBP2NL CTTNBP2 N-terminal-like protein 639 2 3

7833 Q9ULQ0 FA40B FAM40B Protein FAM40B 834 2 3

7071 O95684 FR1OP FGFR1OP FGFR1 oncogene partner 399 2 3

6081 P78318 IGBP1 IGBP1 Immunoglobulin-binding protein 1,

Protein alpha-4 339 3 4

- Q5FBB7 SGOL1 SGOL1, SGO1 Shugoshin-like 1, hSgo1 561 3 4

- - eGFP - - 293 - 34

55  

Table S3. xQuest databases derived from mass spectrometric analysis of non-cross-

linked protein complexes.

Fourteen proteins of the PP2A network were fused to a His6-HA-StrepII-tag and inducibly

expressed in HEK293 cells. Purified protein complexes were subjected to mass spectrometric

analysis and proteins identified by the X!Tandem search algorithm and the Trans Proteomic

Pipeline (Protein Id, UniProt entry and name of identified proteins). PP2A interactors were

separated from contaminant proteins by filtering against a His6-HA-StrepII-eGFP control

purification as described (chapter M4.). Proteins with a score >6 were classified as interactors

(dark blue background). The spectral counts of the identified proteins were normalized to the

bait protein (nsc). The xQuest database was assembled from the 40 proteins with the highest

number of spectral counts (light blue background).

56  

bait PP4C_P60510 bait 2ABA_P63151 bait 2ABG_Q9Y2T4

Protein Id nsc Score Protein Id nsc Score Protein Id nsc Score P60510 PP4C 1.000 100.000 P63151 2ABA 1.000 116.912 P78371 TCPB 1.163 40.369

P78371 TCPB 0.560 37.436 P30153 2AAA 0.699 47.030 P48643 TCPE 1.142 38.640

P50990 TCPQ 0.505 23.500 P67775 PP2AA 0.451 31.333 P50990 TCPQ 1.073 25.929

Q99832 TCPH 0.460 20.000 P62714 PP2AB 0.433 45.841 P49368 TCPG 1.023 46.160

Q9NY27 PP4R2 0.446 100.000 P30154 2AAB 0.223 100.000 Q9Y2T4 2ABG 1.000 100.000

P48643 TCPE 0.443 28.900 P78371 TCPB 0.118 10.051 P40227 TCPZ 0.924 39.075

P40227 TCPZ 0.433 35.250 P50990 TCPQ 0.104 6.214 Q99832 TCPH 0.911 20.560

P17987 TCPA 0.429 28.000 P49368 TCPG 0.096 10.667 P30153 2AAA 0.895 24.485

P49368 TCPG 0.429 37.333 P17987 TCPA 0.086 7.200 P17987 TCPA 0.876 29.640

Q6IN85 P4R3A 0.420 100.000 P48643 TCPE 0.083 6.900 P50991 TCPD 0.853 24.050

Q8TF05 PP4R1 0.379 100.000 Q9Y570 PPME1 0.076 100.000 P67775 PP2AA 0.582 16.400

P50991 TCPD 0.354 19.250 P40227 TCPZ 0.070 7.250 P30154 2AAB 0.330 100.000

P78318 IGBP1 0.276 100.000 Q96E09 F122A 0.062 100.000 Q9BXL8 CDCA4 0.103 100.000

Q16204 CCDC6 0.253 100.000 Q9BQ95 ECSIT 0.052 100.000 Q96RQ3 MCCA 0.723 0.000

Q14738 2A5D 0.218 100.000 Q9BXL8 CDCA4 0.035 100.000 P05165 PCCA 0.696 0.000

P30153 2AAA 0.196 10.343 P11498 PYC 0.448 3.567 P62714 PP2AB 0.641 0.000

Q6NUP7 PP4R4 0.195 100.000 P05165 PCCA 0.382 0.000 Q9HCC0 MCCB 0.591 0.000

Q5MIZ7 P4R3B 0.175 100.000 Q9HCC0 MCCB 0.239 4.070 P11498 PYC 0.573 1.853

P63151 2ABA 0.118 10.807 Q96RQ3 MCCA 0.198 4.566 P07437 TBB5 0.525 4.245

Q66LE6 2ABD 0.054 100.000 P05166 PCCB 0.173 2.828 P05166 PCCB 0.492 0.000

Q6P3S6 FBX42 0.035 100.000 Q13085 ACACA 0.169 4.862 Q13885 TBB2A 0.479 0.000

Q9Y570 PPME1 0.017 100.000 Q12948 FOXC1 0.112 0.000 Q13085 ACACA 0.465 0.000

P30876 RPB2 0.009 100.000 P07437 TBB5 0.109 2.175 P08107 HSP71 0.461 1.414

P07437 TBB5 0.370 5.760 H11111 His-HA-Strep 0.101 0.344 P68371 TBB2C 0.459 3.122

P68371 TBB2C 0.317 4.158 P68371 TBB2C 0.088 0.000 P11142 HSP7C 0.436 1.589

Q9BVA1 TBB2B 0.308 1.971 Q99832 TCPH 0.088 4.867 Q9BQE3 TBA1C 0.346 0.000

Q13885 TBB2A 0.304 0.000 P11142 HSP7C 0.084 0.754 P68363 TBA1B 0.342 3.500

P68363 TBA1B 0.244 4.805 P68363 TBA1B 0.083 2.085 Q71U36 TBA1A 0.328 0.000

Q71U36 TBA1A 0.239 0.000 Q9BQE3 TBA1C 0.081 0.000 Q9BVA1 TBB2B 0.324 0.000

Q9BQE3 TBA1C 0.239 0.000 P14618 KPYM 0.079 1.814 P15636 LysC 0.253 0.000

P08107 HSP71 0.222 1.314 P08107 HSP71 0.079 0.598 Q9BUF5 TBB6 0.228 0.000

P11498 PYC 0.199 1.243 P50991 TCPD 0.077 5.333 P38646 GRP75 0.227 2.288

P11142 HSP7C 0.181 1.271 P04264 K2C1 0.074 0.900 P27708 PYR1 0.216 3.366

P68104 EF1A1 0.167 5.408 Q00839 HNRPU 0.072 0.000 P10809 CH60 0.188 0.000

H11111 His-HA-Strep 0.164 0.438 P13645 K1C10 0.067 0.000 O14654 IRS4 0.183 3.800

P27708 PYR1 0.149 4.460 P13807 GYS1 0.063 0.000 P68104 EF1A1 0.179 3.007

Q9BUF5 TBB6 0.130 1.667 P35908 K22E 0.058 0.000 P54652 HSP72 0.177 0.000

Q08211 DHX9 0.124 0.000 P46781 RS9 0.058 0.000 H11111 His-HA-Strep 0.167 0.231

O14654 IRS4 0.121 4.858 P81274 GPSM2 0.058 0.000 P04264 K2C1 0.151 0.000

P04040 CATA 0.110 0.000 Q71U36 TBA1A 0.058 0.000 P35908 K22E 0.148 0.000

Q8WWM7 ATX2L 0.097 1.353 P35527 K1C9 0.050 0.000 P11021 GRP78 0.140 1.161

P38646 GRP75 0.089 1.728 Q9Y375 CIA30 0.049 0.000 P13645 K1C10 0.117 0.000

P49411 EFTU 0.087 0.000 Q14980 NUMA1 0.047 0.000 P52272 HNRPM 0.099 1.400

P81274 GPSM2 0.078 0.000 Q8WWM7 ATX2L 0.044 0.795 P02538 K2C6A 0.098 0.000

P11021 GRP78 0.075 1.200 P11021 GRP78 0.043 0.882 P35527 K1C9 0.089 0.000

P52272 HNRPM 0.075 2.042 Q92841 DDX17 0.043 0.000 O00763 ACACB 0.080 0.000

P11182 ODB2 0.072 0.351 P13051 UNG 0.040 0.000 O95831 AIFM1 0.080 0.000

P35527 K1C9 0.064 0.000 P62701 RS4X 0.037 2.316 P08779 K1C16 0.080 0.000

P04264 K2C1 0.064 0.000 P68104 EF1A1 0.036 1.489 P14618 KPYM 0.080 0.000

P00367 DHE3 0.060 4.875 P17844 DDX5 0.036 0.000 Q13242 SFRS9 0.080 0.000

Q14980 NUMA1 0.060 0.000 Q06830 PRDX1 0.036 0.000 Q9Y230 RUVB2 0.074 0.764

P62701 RS4X 0.058 2.839 O60548 FOXD2 0.034 0.000 P08238 HS90B 0.071 0.000

P13645 K1C10 0.055 0.000 P04406 G3P 0.032 0.000 P02533 K1C14 0.066 0.000

P35908 K22E 0.055 0.000 P10809 CH60 0.032 0.000 P36776 LONM 0.066 0.000

Q9HCC0 MCCB 0.051 0.000 Q13242 SFRS9 0.031 2.773 Q9Y265 RUVB1 0.066 2.114

P31689 DNJA1 0.049 1.123 P62805 H4 0.030 2.252 P31689 DNJA1 0.064 0.758

P30154 2AAB 0.048 0.000 P38646 GRP75 0.029 0.715 P13647 K2C5 0.062 0.000

Q00839 HNRPU 0.048 1.350 P06899 H2B1J 0.029 0.000 P00367 DHE3 0.060 2.550

P02533 K1C14 0.046 0.000 P08670 VIME 0.029 0.000 Q8WWM7 ATX2L 0.059 0.425

P15636 LysC 0.046 0.000 P14866 HNRPL 0.029 0.000 P07900 HS90A 0.058 0.000

P62280 RS11 0.043 3.394 P46976 GLYG 0.029 0.000 Q9NUC0 SRTD4 0.058 0.000

P08670 VIME 0.043 1.311 P62753 RS6 0.029 0.000 P62701 RS4X 0.055 0.000

P31943 HNRH1 0.040 2.080 Q15233 NONO 0.029 0.000 O95816 BAG2 0.055 1.459

P12755 SKI 0.040 0.542 Q9UJU5 FOXD3 0.029 0.000 P08670 VIME 0.053 0.000

Q92616 GCN1L 0.039 0.000 Q66LE6 2ABD 0.028 0.000 P11182 ODB2 0.053 0.000

P16104 H2AX 0.037 0.000 P04075 ALDOA 0.025 0.000 P49411 EFTU 0.050 0.000

P13647 K2C5 0.037 0.000 P06744 G6PI 0.025 0.000 P60709 ACTB 0.048 0.457

P04259 K2C6B 0.037 0.000 P08238 HS90B 0.025 0.000 P31943 HNRH1 0.047 0.000

Q96RQ3 MCCA 0.037 0.000 P08621 RU17 0.025 0.000 P23527 H2B1O 0.044 0.000

P05166 PCCB 0.037 0.000 P18621 RL17 0.025 0.000 P35998 PRS7 0.044 0.000

57  

bait PP2AB_P62714 bait 2A5D_Q14738 bait 2A5E_Q16537

Protein Id nsc Score Protein Id nsc Score Protein Id nsc Score P62714 PP2AB 1.000 114.743 Q14738 2A5D 1.000 100.000 P30153 2AAA 1.866 79.030

P30153 2AAA 0.576 42.036 P30153 2AAA 0.579 28.606 P67775 PP2AA 1.529 66.750

Q14738 2A5D 0.552 100.000 P67775 PP2AA 0.465 23.667 P62714 PP2AB 1.511 100.571

P30154 2AAB 0.221 100.000 P62714 PP2AB 0.458 35.556 Q16537 2A5E 1.000 100.000

Q13362 2A5G 0.218 100.000 P30154 2AAB 0.270 100.000 P30154 2AAB 0.649 100.000

P63151 2ABA 0.215 27.284 Q13136 LIPA1 0.115 100.000 Q5FBB7 SGOL1 0.183 100.000

Q8N201 INT1 0.204 100.000 P60510 PP4C 0.044 100.000 O94964 CT117 0.141 100.000

Q13136 LIPA1 0.181 100.000 Q9HCC0 MCCB 0.646 0.000 Q01105 SET 0.086 6.176

Q96HW7 INT4 0.153 100.000 P11498 PYC 0.637 3.720 Q562F6 SGOL2 0.080 100.000

P78318 IGBP1 0.150 100.000 Q96RQ3 MCCA 0.597 0.000 Q5TF21 CF174 0.069 100.000

Q9UL03 INT6 0.139 100.000 P05165 PCCA 0.439 4.358 O94988 FA13A 0.058 100.000

Q9NV88 INT9 0.123 100.000 P05166 PCCB 0.304 3.653 Q14674 ESPL1 0.049 100.000

Q9NRL3 STRN4 0.104 100.000 H11111 His-HA-Strep 0.231 0.577 Q9NTK1 DEPP 0.023 100.000

Q9NVM9 M89BB 0.098 100.000 Q13085 ACACA 0.180 4.655 P11498 PYC 0.769 3.853

Q9NVH2 INT7 0.097 100.000 P08107 HSP71 0.126 0.698 Q96RQ3 MCCA 0.624 0.000

P78371 TCPB 0.097 8.985 P07437 TBB5 0.113 1.649 Q9HCC0 MCCB 0.578 0.000

Q9Y570 PPME1 0.095 100.000 P04264 K2C1 0.106 0.944 P05165 PCCA 0.449 0.000

Q13033 STRN3 0.092 100.000 Q71U36 TBA1A 0.106 0.000 P05166 PCCB 0.352 0.000

P40227 TCPZ 0.092 8.175 P68363 TBA1B 0.105 1.934 P11142 HSP7C 0.157 0.000

Q16204 CCDC6 0.091 100.000 P11142 HSP7C 0.103 0.678 Q13085 ACACA 0.153 4.138

Q66LE6 2ABD 0.090 100.000 P13647 K2C5 0.093 0.000 P08107 HSP71 0.139 0.662

Q86XL3 ANKL2 0.088 100.000 Q9BVA1 TBB2B 0.093 0.000 H11111 His-HA-Strep 0.137 0.294

Q9H0H0 INT2 0.087 100.000 P68371 TBB2C 0.092 1.125 Q71U36 TBA1A 0.137 0.000

Q5TA45 INT11 0.085 100.000 P35908 K22E 0.086 0.000 P07437 TBB5 0.122 1.530

Q9P2B4 CT2NL 0.082 100.000 P02533 K1C14 0.079 0.000 P11182 ODB2 0.106 0.000

O43815 STRN 0.082 100.000 P13645 K1C10 0.076 0.000 P68371 TBB2C 0.105 1.105

P17987 TCPA 0.068 6.120 P11021 GRP78 0.074 1.102 P68363 TBA1B 0.101 1.602

P48643 TCPE 0.066 6.000 Q92841 DDX17 0.069 0.000 P04264 K2C1 0.099 0.755

Q6P9B9 INT5 0.064 100.000 P04259 K2C6B 0.064 0.000 Q9Y4B5 K0802 0.094 0.000

P49368 TCPG 0.062 7.520 P68104 EF1A1 0.054 1.637 P15636 LysC 0.092 0.000

Q5THK1 PR14L 0.060 100.000 P78318 IGBP1 0.054 0.000 Q8WWM7 ATX2L 0.088 0.988

Q5VSL9 FA40A 0.058 100.000 Q13242 SFRS9 0.054 0.000 P35527 K1C9 0.086 0.000

Q16537 2A5E 0.057 100.000 P35527 K1C9 0.052 0.678 P62701 RS4X 0.077 0.000

Q75QN2 INT8 0.055 100.000 Q00839 HNRPU 0.052 0.000 P11021 GRP78 0.072 0.000

O75145 LIPA3 0.050 100.000 P39019 RS19 0.049 0.000 P68104 EF1A1 0.069 1.786

Q9Y3A3 MOBL3 0.044 100.000 O75145 LIPA3 0.047 0.000 P13645 K1C10 0.067 0.727

P22830 HEMH 0.034 100.000 Q8WWM7 ATX2L 0.046 0.601 Q9BQE3 TBA1C 0.063 0.000

Q9BWN1 PRR14 0.028 100.000 P11182 ODB2 0.044 0.000 P35908 K22E 0.055 0.862

Q96SY0 CO044 0.025 100.000 P38646 GRP75 0.043 0.775 Q13011 ECH1 0.054 0.000

Q13085 ACACA 0.428 0.000 P23246 SFPQ 0.039 0.000 P12755 SKI 0.052 0.000

P11498 PYC 0.327 2.823 Q9UQE7 SMC3 0.039 0.000 Q7Z7L8 AG2 0.049 0.000

P08670 VIME 0.186 0.000 P08670 VIME 0.038 1.077 P08779 K1C16 0.046 0.000

Q9HCC0 MCCB 0.144 0.000 P17844 DDX5 0.034 0.000 P61247 RS3A 0.046 0.000

P07437 TBB5 0.133 2.868 P62701 RS4X 0.034 0.000 Q9H246 CA021 0.043 0.000

H11111 His-HA-Strep 0.122 0.000 Q7Z794 K2C1B 0.034 0.000 Q92974 ARHG2 0.040 0.000

Q9BVA1 TBB2B 0.118 0.000 P12755 SKI 0.029 0.375 Q5SYE7 NHSL1 0.034 0.000

P05165 PCCA 0.115 0.000 P08238 HS90B 0.029 0.000 P08670 VIME 0.031 0.000

P04350 TBB4 0.113 0.000 P08621 RU17 0.029 0.000 P38646 GRP75 0.031 0.000

P68371 TBB2C 0.108 1.953 P52272 HNRPM 0.029 0.000 O15027 SC16A 0.029 0.000

Q71U36 TBA1A 0.101 0.000 Q14683 SMC1A 0.029 0.000 P0C0S8 H2A1 0.029 0.000

Q96RQ3 MCCA 0.099 0.000 Q15365 PCBP1 0.029 0.000 P46781 RS9 0.029 0.000

Q9BQE3 TBA1C 0.098 0.000 O60814 H2B1K 0.027 0.000 P81274 GPSM2 0.029 0.000

P68363 TBA1B 0.094 2.557 P78371 TCPB 0.026 1.641 Q69YH5 CDCA2 0.029 0.000

P08107 HSP71 0.085 0.696 P62805 H4 0.025 1.351 P52272 HNRPM 0.026 0.000

O00763 ACACB 0.080 0.000 P0C0S8 H2A1 0.025 0.000 P43243 MATR3 0.025 0.625

P68032 ACTC 0.080 0.000 P26599 PTBP1 0.025 0.000 P00761 TRYP 0.025 0.207

P50990 TCPQ 0.078 5.057 P31943 HNRH1 0.025 0.000 P04259 K2C6B 0.023 0.000

P05166 PCCB 0.077 0.000 P43243 MATR3 0.025 0.000 P39019 RS19 0.023 0.000

Q8TF05 PP4R1 0.076 0.000 P62244 RS15A 0.025 0.000 Q5T4S7 UBR4 0.023 0.000

Q16643 DREB 0.070 0.000 P62280 RS11 0.025 0.000 O60814 H2B1K 0.020 0.000

Q5FBB7 SGOL1 0.069 0.000 Q08211 DHX9 0.025 0.000 P31943 HNRH1 0.020 0.000

Q99832 TCPH 0.066 4.000 Q13011 ECH1 0.025 0.000 P62805 H4 0.020 0.000

P11142 HSP7C 0.064 0.620 Q8IUD2 RB6I2 0.025 0.000 Q8IUD2 RB6I2 0.017 0.750

P60709 ACTB 0.063 0.000 P04406 G3P 0.020 0.000 O14654 IRS4 0.017 0.000

Q5JSJ4 DX26B 0.062 0.000 P23527 H2B1O 0.020 0.000 P13647 K2C5 0.017 0.000

P03243 E1BL 0.056 0.000 P26373 RL13 0.020 0.000 P26599 PTBP1 0.017 0.000

Q68E01 INT3 0.055 0.000 P28799 GRN 0.020 0.000 P27635 RL10 0.017 0.000

P50991 TCPD 0.054 4.050 P40227 TCPZ 0.020 0.000 P30050 RL12 0.017 0.000

Q9UHB6 LIMA1 0.053 0.000 P62910 RL32 0.020 0.000 P31942 HNRH3 0.017 0.000

P68104 EF1A1 0.049 2.203 Q15366 PCBP2 0.020 0.000 P60709 ACTB 0.017 0.000

58  

bait 2A5G_Q13362 bait 2AAB_P30154 bait SGOL1_Q5FBB7

Protein Id nsc Score Protein Id nsc Score Protein Id nsc Score P30153 2AAA 1.280 89.778 P30154 2AAB 1.000 100.000 Q5FBB7 SGOL1 1.000 100.000

Q13362 2A5G 1.000 100.000 Q14738 2A5D 0.408 100.000 P30153 2AAA 0.996 32.303

P67775 PP2AA 0.775 56.083 P62714 PP2AB 0.359 11.714 P62714 PP2AB 0.768 39.143

P62714 PP2AB 0.760 83.810 P63151 2ABA 0.224 8.105 Q13362 2A5G 0.531 100.000

P30154 2AAB 0.540 100.000 Q13033 STRN3 0.195 100.000 P30154 2AAB 0.402 100.000

Q13136 LIPA1 0.408 100.000 Q9NRL3 STRN4 0.117 100.000 Q14738 2A5D 0.378 100.000

Q14674 ESPL1 0.162 100.000 Q9Y4R8 TELO2 0.114 100.000 Q16537 2A5E 0.249 100.000

O75145 LIPA3 0.154 100.000 O43815 STRN 0.102 100.000 Q15172 2A5A 0.239 100.000

Q5THK1 PR14L 0.144 100.000 O94927 HAUS5 0.102 100.000 Q01105 SET 0.179 9.882

Q69YH5 CDCA2 0.123 100.000 P30876 RPB2 0.085 100.000 Q15173 2A5B 0.101 100.000

Q5FBB7 SGOL1 0.105 100.000 Q9Y3A3 MOBL3 0.067 100.000 Q96RQ3 MCCA 0.968 0.000

O75334 LIPA2 0.100 100.000 Q5VSL9 FA40A 0.055 100.000 P67775 PP2AA 0.927 0.000

Q9BWN1 PRR14 0.083 100.000 P11498 PYC 1.496 3.679 P11498 PYC 0.893 3.428

P51959 CCNG1 0.047 100.000 Q71U36 TBA1A 1.329 0.000 Q9HCC0 MCCB 0.890 0.000

Q9NTK1 DEPP 0.010 100.000 P07437 TBB5 1.029 5.360 P05165 PCCA 0.662 0.000

H11111 His-HA-Strep 0.147 0.524 Q9BVA1 TBB2B 1.022 0.000 P05166 PCCB 0.349 0.000

P11498 PYC 0.127 1.052 Q96RQ3 MCCA 0.987 0.000 P08107 HSP71 0.252 0.918

P08107 HSP71 0.124 0.979 P04350 TBB4 0.939 0.000 Q13085 ACACA 0.252 0.000

P07437 TBB5 0.123 2.557 P68371 TBB2C 0.921 4.761 P11142 HSP7C 0.204 0.880

P68371 TBB2C 0.118 2.049 P68363 TBA1B 0.854 5.599 P07437 TBB5 0.166 1.595

Q9BVA1 TBB2B 0.111 0.000 Q9HCC0 MCCB 0.776 4.080 P04264 K2C1 0.164 0.958

P68363 TBA1B 0.098 2.569 Q13885 TBB2A 0.754 0.000 H11111 His-HA-Strep 0.159 0.261

P11142 HSP7C 0.090 0.840 Q9BQE3 TBA1C 0.752 2.633 P11182 ODB2 0.157 0.000

Q71U36 TBA1A 0.090 0.000 P08107 HSP71 0.691 1.611 Q9BQE3 TBA1C 0.157 0.000

P11021 GRP78 0.058 1.225 P27708 PYR1 0.577 5.759 P68371 TBB2C 0.140 1.130

P05165 PCCA 0.055 0.000 P11142 HSP7C 0.571 1.583 P68363 TBA1B 0.127 1.541

P05166 PCCB 0.055 0.000 P05165 PCCA 0.539 2.256 Q9BVA1 TBB2B 0.127 0.000

P35908 K22E 0.048 0.000 P05166 PCCB 0.475 2.401 P15636 LysC 0.117 0.000

P15636 LysC 0.045 0.000 O14654 IRS4 0.469 5.949 P13645 K1C10 0.116 0.966

Q96RQ3 MCCA 0.045 0.000 Q9BUF5 TBB6 0.429 2.162 P11021 GRP78 0.114 1.121

P38646 GRP75 0.044 1.132 Q92616 GCN1L 0.411 5.875 P68104 EF1A1 0.103 2.047

Q9HCC0 MCCB 0.043 0.000 P68104 EF1A1 0.373 4.763 Q8WWM7 ATX2L 0.099 0.854

P13645 K1C10 0.043 0.769 P04264 K2C1 0.350 1.307 P38646 GRP75 0.097 0.000

P04264 K2C1 0.043 0.537 P11021 GRP78 0.318 2.003 P35908 K22E 0.082 0.981

P11182 ODB2 0.036 0.000 Q13085 ACACA 0.315 4.190 P35527 K1C9 0.079 0.667

P68104 EF1A1 0.036 1.538 P38646 GRP75 0.297 2.279 Q13011 ECH1 0.075 0.000

P08238 HS90B 0.035 0.000 P67775 PP2AA 0.295 0.000 P08670 VIME 0.057 0.000

Q9BUF5 TBB6 0.033 0.000 P49327 FAS 0.265 4.333 P02533 K1C14 0.052 0.000

Q14974 IMB1 0.031 0.000 P08670 VIME 0.257 3.091 P46781 RS9 0.052 0.000

P35527 K1C9 0.031 0.000 P78527 PRKDC 0.236 3.375 Q9ULV4 COR1C 0.052 0.000

Q8WWM7 ATX2L 0.030 0.558 P35527 K1C9 0.230 1.255 Q00839 HNRPU 0.047 0.000

P52272 HNRPM 0.028 0.000 Q8WWM7 ATX2L 0.222 1.224 P52272 HNRPM 0.045 0.000

P07900 HS90A 0.028 0.000 P00367 DHE3 0.216 5.063 P60709 ACTB 0.040 0.000

O94988 FA13A 0.026 0.000 P11182 ODB2 0.210 0.404 P62269 RS18 0.040 0.000

P12755 SKI 0.026 0.000 P13645 K1C10 0.207 1.106 O15027 SC16A 0.037 0.000

P52292 IMA2 0.024 0.000 P36578 RL4 0.192 2.373 P00367 DHE3 0.037 0.000

O14654 IRS4 0.024 0.000 P62701 RS4X 0.187 0.000 P12755 SKI 0.037 0.000

P13647 K2C5 0.024 0.000 P08238 HS90B 0.184 1.396 P62280 RS11 0.037 0.000

Q15233 NONO 0.024 0.000 Q9Y2X3 NOP58 0.167 0.000 P62424 RL7A 0.037 0.000

O15027 SC16A 0.021 0.000 P07900 HS90A 0.166 1.292 P62701 RS4X 0.037 0.000

Q00839 HNRPU 0.017 0.000 O00567 NOP56 0.159 0.000 Q9Y230 RUVB2 0.037 0.000

P27708 PYR1 0.017 0.000 P40939 ECHA 0.159 0.000 O14654 IRS4 0.034 0.000

Q7Z7L8 AG2 0.014 0.000 P25705 ATPA 0.157 3.375 P26599 PTBP1 0.034 0.000

P81274 GPSM2 0.014 0.000 P35908 K22E 0.157 1.203 Q5T4S7 UBR4 0.034 0.000

P43243 MATR3 0.014 0.000 P17987 TCPA 0.155 0.000 Q92841 DDX17 0.034 0.000

Q5SYE7 NHSL1 0.014 0.000 P10809 CH60 0.146 0.810 O60814 H2B1K 0.030 0.000

Q8IUD2 RB6I2 0.014 1.000 P15636 LysC 0.146 0.000 P02538 K2C6A 0.030 0.000

P62280 RS11 0.014 0.000 P13639 EF2 0.143 2.450 P08238 HS90B 0.030 0.000

P46781 RS9 0.014 0.000 P62280 RS11 0.136 0.000 P22087 FBRL 0.030 0.000

P09001 RM03 0.012 0.000 P62829 RL23 0.128 3.808 P30050 RL12 0.030 0.000

P62701 RS4X 0.012 0.000 P23396 RS3 0.128 2.809 P31943 HNRH1 0.030 0.000

P00761 TRYP 0.012 0.000 P62753 RS6 0.128 0.000 P39019 RS19 0.030 0.000

Q92616 GCN1L 0.010 0.000 Q8N201 INT1 0.128 0.000 P62750 RL23A 0.030 0.000

O60814 H2B1K 0.010 0.000 P31689 DNJA1 0.125 1.132 Q15366 PCBP2 0.030 0.000

P31943 HNRH1 0.010 0.000 P52272 HNRPM 0.121 0.000 Q9Y490 TLN1 0.030 0.000

Q7RTS7 K2C74 0.010 0.000 P55060 XPO2 0.121 0.000 P00761 TRYP 0.027 0.000

Q06830 PRDX1 0.010 0.000 H11111 His-HA-Strep 0.120 0.126 P43243 MATR3 0.026 0.000

P62750 RL23A 0.010 0.000 P27635 RL10 0.117 0.000 P62081 RS7 0.026 0.000

P40227 TCPZ 0.010 0.000 P46781 RS9 0.111 0.000 P78318 IGBP1 0.026 0.000

P62995 TRA2B 0.010 0.000 Q13362 2A5G 0.109 0.000 P04637 P53 0.022 0.000

59  

bait FA40B_Q9ULQ0 bait FR1OP_O95684 bait IGBP1_P78318

Protein Id nsc Score Protein Id nsc Score Protein Id nsc Score Q9ULQ0 FA40B 1.000 100.000 O95684 FR1OP 1.000 100.000 P78318 IGBP1 1.000 100.000

Q13557 KCC2D 0.169 100.000 Q5VT06 CE350 0.643 100.000 P78371 TCPB 0.324 38.615

Q13555 KCC2G 0.141 100.000 P30153 2AAA 0.154 8.081 P40227 TCPZ 0.236 34.313

Q96C01 F136A 0.089 100.000 Q969Q6 P2R3C 0.145 100.000 Q99832 TCPH 0.204 15.800

Q9NRL3 STRN4 0.080 100.000 P62714 PP2AB 0.102 8.381 P50990 TCPQ 0.194 16.125

Q13033 STRN3 0.061 100.000 P30154 2AAB 0.060 100.000 P48643 TCPE 0.193 22.425

P11498 PYC 0.845 2.916 O60610 DIAP1 0.052 100.000 P17987 TCPA 0.187 21.675

P07437 TBB5 0.554 4.780 P11021 GRP78 0.274 4.360 P49368 TCPG 0.166 25.700

Q9BVA1 TBB2B 0.486 0.000 H11111 His-HA-Strep 0.268 0.712 P67775 PP2AA 0.159 15.375

P68371 TBB2C 0.471 3.415 P08107 HSP71 0.242 1.423 P50991 TCPD 0.145 14.063

P68363 TBA1B 0.452 4.926 P11142 HSP7C 0.231 1.615 P62714 PP2AB 0.109 16.095

Q9HCC0 MCCB 0.429 3.170 P07437 TBB5 0.198 3.083 P60510 PP4C 0.085 100.000

Q13885 TBB2A 0.421 1.126 P11498 PYC 0.192 1.195 O00743 PPP6 0.054 100.000

Q9BQE3 TBA1C 0.404 1.986 P68371 TBB2C 0.189 2.471 P11498 PYC 0.250 2.775

P04350 TBB4 0.395 0.000 P04350 TBB4 0.189 0.000 P05166 PCCB 0.187 0.000

P11142 HSP7C 0.360 1.400 P04264 K2C1 0.174 1.641 Q96RQ3 MCCA 0.187 0.000

P08107 HSP71 0.332 1.088 Q9BVA1 TBB2B 0.163 1.039 P05165 PCCA 0.183 0.000

Q96RQ3 MCCA 0.310 3.845 P68363 TBA1B 0.158 3.113 Q9HCC0 MCCB 0.174 0.000

P05165 PCCA 0.294 1.724 Q13885 TBB2A 0.157 0.000 P07437 TBB5 0.154 4.284

Q8WWM7 ATX2L 0.252 1.954 Q9BQE3 TBA1C 0.152 0.000 Q9BVA1 TBB2B 0.142 0.000

O14654 IRS4 0.238 4.919 P38646 GRP75 0.149 2.890 Q13885 TBB2A 0.136 0.000

P68104 EF1A1 0.230 4.118 Q71U36 TBA1A 0.141 0.000 P68371 TBB2C 0.133 3.104

P27708 PYR1 0.227 3.770 P27708 PYR1 0.135 4.046 P68363 TBA1B 0.125 4.397

Q9BUF5 TBB6 0.175 1.235 P35908 K22E 0.117 2.258 H11111 His-HA-Strep 0.121 0.574

H11111 His-HA-Strep 0.175 0.258 P02768 ALBU 0.115 0.000 Q71U36 TBA1A 0.116 0.000

Q92616 GCN1L 0.162 0.000 P68104 EF1A1 0.102 3.275 Q9BQE3 TBA1C 0.116 1.827

P05166 PCCB 0.161 1.139 P13645 K1C10 0.102 1.371 P11142 HSP7C 0.085 1.066

Q13242 SFRS9 0.158 0.000 P34931 HS71L 0.097 0.000 P08107 HSP71 0.085 0.897

P11021 GRP78 0.147 1.298 P67775 PP2AA 0.090 0.000 P27708 PYR1 0.066 3.552

P38646 GRP75 0.139 1.489 P35527 K1C9 0.086 1.186 P04264 K2C1 0.060 1.013

Q13085 ACACA 0.133 2.483 P54652 HSP72 0.074 0.000 P68104 EF1A1 0.056 3.200

P35580 MYH10 0.133 0.000 P00367 DHE3 0.069 0.000 Q9BUF5 TBB6 0.048 1.103

Q5VSL9 FA40A 0.133 0.000 Q7Z7L1 SLN11 0.069 0.000 P08670 VIME 0.047 0.000

P35579 MYH9 0.125 0.000 Q8WWM7 ATX2L 0.062 0.859 O14654 IRS4 0.044 3.136

Q13554 KCC2B 0.125 0.000 O95831 AIFM1 0.057 3.524 P68032 ACTC 0.044 0.000

P49411 EFTU 0.120 0.000 P04259 K2C6B 0.055 0.000 P11021 GRP78 0.043 0.937

P52272 HNRPM 0.119 1.792 P52272 HNRPM 0.048 1.292 P11182 ODB2 0.041 0.000

P00367 DHE3 0.114 5.125 P04040 CATA 0.046 0.000 P15636 LysC 0.041 0.000

P49327 FAS 0.111 2.540 P13646 K1C13 0.042 0.000 P35527 K1C9 0.039 0.953

P31689 DNJA1 0.111 1.404 Q96HS1 PGAM5 0.042 0.000 Q13085 ACACA 0.039 0.000

P08670 VIME 0.108 1.826 P15636 LysC 0.039 0.000 Q92526 TCPW 0.039 0.000

Q8N163 K1967 0.102 5.556 P13647 K2C5 0.038 0.967 P38646 GRP75 0.032 0.000

P11182 ODB2 0.102 0.277 Q92616 GCN1L 0.037 1.333 P13645 K1C10 0.032 0.763

P08238 HS90B 0.094 1.005 P12755 SKI 0.037 0.500 P35908 K22E 0.028 0.981

O95831 AIFM1 0.083 2.857 P12236 ADT3 0.037 0.000 P27635 RL10 0.028 0.000

P15636 LysC 0.083 1.250 P42704 LPPRC 0.037 0.000 P62701 RS4X 0.027 0.000

P62701 RS4X 0.083 0.000 Q13576 IQGA2 0.037 0.000 P52272 HNRPM 0.026 0.000

Q9Y265 RUVB1 0.083 0.000 P02533 K1C14 0.035 0.000 Q13011 ECH1 0.026 0.000

P62280 RS11 0.079 0.000 P05141 ADT2 0.035 0.000 P25705 ATPA 0.024 0.000

O60884 DNJA2 0.075 0.750 O14654 IRS4 0.032 1.291 P60709 ACTB 0.024 0.782

P35527 K1C9 0.075 0.000 P60709 ACTB 0.032 0.592 P22087 FBRL 0.022 0.000

P61254 RL26 0.075 0.000 P08238 HS90B 0.032 0.000 P62280 RS11 0.022 0.000

P78527 PRKDC 0.075 0.000 Q00839 HNRPU 0.032 0.000 P00367 DHE3 0.021 0.000

Q7Z417 NUFP2 0.075 0.000 Q16537 2A5E 0.032 0.000 P36578 RL4 0.021 0.000

P62805 H4 0.072 2.342 P10809 CH60 0.030 0.000 P43243 MATR3 0.021 0.000

Q9Y230 RUVB2 0.072 0.788 Q13085 ACACA 0.030 0.000 Q8WWM7 ATX2L 0.019 0.467

P60709 ACTB 0.072 0.733 Q9Y265 RUVB1 0.030 0.000 O00567 NOP56 0.018 0.000

P12755 SKI 0.072 0.542 P10398 ARAF 0.028 0.000 O15027 SC16A 0.018 0.000

P10809 CH60 0.071 0.000 P15880 RS2 0.028 0.000 P46779 RL28 0.018 0.000

P43243 MATR3 0.066 1.154 P78371 TCPB 0.028 0.000 Q08211 DHX9 0.018 0.000

P07900 HS90A 0.066 0.725 Q16514 TAF12 0.028 0.000 Q92616 GCN1L 0.018 0.000

P05141 ADT2 0.066 0.000 Q92841 DDX17 0.028 0.000 Q9Y2X3 NOP58 0.018 0.000

P13639 EF2 0.066 0.000 Q92878 RAD50 0.028 0.000 P31689 DNJA1 0.017 0.711

P17987 TCPA 0.066 0.000 Q8IUD2 RB6I2 0.023 1.250 P49327 FAS 0.017 1.238

P39019 RS19 0.066 0.000 P08670 VIME 0.023 0.702 Q3ZCQ8 TIM50 0.017 0.000

Q13435 SF3B2 0.066 0.000 P07814 SYEP 0.023 0.000 Q9ULV4 COR1C 0.017 0.000

Q7Z7L1 SLN11 0.066 0.000 P31943 HNRH1 0.023 0.000 O95831 AIFM1 0.015 0.000

Q00839 HNRPU 0.064 1.002 P49327 FAS 0.023 0.000 P05141 ADT2 0.015 0.000

O15027 SC16A 0.062 0.000 P62701 RS4X 0.023 0.000 P13647 K2C5 0.015 0.000

P13645 K1C10 0.062 0.000 P81605 DCD 0.023 0.000 P52597 HNRPF 0.015 0.000

60  

bait CT2NL_Q9P2B4 bait PP2AA_P67775

Protein Id nsc Score Protein Id nsc Score Q9P2B4 CT2NL 1.000 100.000 P67775 PP2AA 1.000 59.167

Q9NRL3 STRN4 0.319 100.000 P30153 2AAA 0.854 48.970

P63167 DYL1 0.294 100.000 Q14738 2A5D 0.675 100.000

O43815 STRN 0.257 100.000 Q13136 LIPA1 0.406 100.000

Q5VSL9 FA40A 0.209 100.000 P30154 2AAB 0.321 100.000

Q13033 STRN3 0.198 100.000 P63151 2ABA 0.318 31.719

P30153 2AAA 0.139 14.949 Q13362 2A5G 0.304 100.000

Q8WZ74 CTTB2 0.102 100.000 Q8N201 INT1 0.275 100.000

Q9Y3A3 MOBL3 0.102 100.000 Q86XL3 ANKL2 0.251 100.000

P67775 PP2AA 0.088 9.750 Q9UL03 INT6 0.249 100.000

P62714 PP2AB 0.087 14.730 Q96HW7 INT4 0.214 100.000

Q9ULQ0 FA40B 0.084 100.000 P78318 IGBP1 0.204 100.000

Q96FJ2 DYL2 0.050 100.000 Q9NV88 INT9 0.203 100.000

P30154 2AAB 0.050 100.000 P78371 TCPB 0.199 14.462

O95819 M4K4 0.040 100.000 Q9NVH2 INT7 0.197 100.000

Q9P289 MST4 0.032 100.000 P50990 TCPQ 0.194 9.857

Q9Y6E0 STK24 0.026 100.000 Q16204 CCDC6 0.170 100.000

Q9BUL8 PDC10 0.014 100.000 Q9NVM9 M89BB 0.170 100.000

P11498 PYC 0.179 2.276 P48643 TCPE 0.169 12.000

P08107 HSP71 0.114 1.369 Q9NRL3 STRN4 0.163 100.000

Q9BVA1 TBB2B 0.090 0.000 P17987 TCPA 0.161 11.400

P07437 TBB5 0.090 2.844 Q9Y570 PPME1 0.158 100.000

P11142 HSP7C 0.086 1.228 P49368 TCPG 0.158 14.933

P38646 GRP75 0.084 3.336 P50991 TCPD 0.155 9.167

Q8WWM7 ATX2L 0.080 2.276 P40227 TCPZ 0.152 13.500

P68371 TBB2C 0.075 1.989 Q99832 TCPH 0.149 7.067

P11021 GRP78 0.074 2.401 Q66LE6 2ABD 0.148 100.000

P68363 TBA1B 0.067 2.690 P22830 HEMH 0.144 100.000

Q71U36 TBA1A 0.066 0.000 Q13033 STRN3 0.144 100.000

Q9BQE3 TBA1C 0.058 0.000 Q9P2B4 CT2NL 0.144 100.000

P68104 EF1A1 0.056 3.672 O43815 STRN 0.142 100.000

Q9HCC0 MCCB 0.053 1.452 Q5TA45 INT11 0.138 100.000

P05165 PCCA 0.053 0.000 Q9H0H0 INT2 0.137 100.000

H11111 His-HA-Strep 0.052 0.282 Q5FBB7 SGOL1 0.137 100.000

Q96RQ3 MCCA 0.047 0.000 O75145 LIPA3 0.135 100.000

P78371 TCPB 0.037 5.026 Q5THK1 PR14L 0.135 100.000

P11182 ODB2 0.034 0.336 Q5VSL9 FA40A 0.135 100.000

P05166 PCCB 0.030 0.786 Q6P9B9 INT5 0.101 100.000

P04264 K2C1 0.029 0.552 Q68E01 INT3 0.100 100.000

Q9H3G5 CPVL 0.028 4.111 Q75QN2 INT8 0.092 100.000

P08670 VIME 0.028 1.733 Q96SY0 CO044 0.086 100.000

P49368 TCPG 0.027 4.800 Q9NVR2 INT10 0.086 100.000

P40227 TCPZ 0.027 4.500 Q16537 2A5E 0.077 100.000

Q13362 2A5G 0.025 0.000 Q96CB8 INT12 0.073 100.000

P50990 TCPQ 0.024 2.286 Q9Y3A3 MOBL3 0.070 100.000

P52272 HNRPM 0.024 1.333 Q8TF05 PP4R1 0.063 100.000

Q9BUF5 TBB6 0.024 0.627 Q9BWN1 PRR14 0.046 100.000

P17987 TCPA 0.023 3.100 P24928 RPB1 0.032 100.000

P13645 K1C10 0.023 0.000 P51959 CCNG1 0.028 100.000

P15636 LysC 0.021 0.000 O95684 FR1OP 0.027 100.000

Q7Z417 NUFP2 0.020 1.929 Q15173 2A5B 0.025 100.000

Q00839 HNRPU 0.020 0.000 Q69YH5 CDCA2 0.025 100.000

P62805 H4 0.019 0.000 Q8WZ74 CTTB2 0.025 100.000

P48643 TCPE 0.018 2.400 Q9NRY2 SOSSC 0.024 100.000

O14654 IRS4 0.018 0.000 P30876 RPB2 0.021 100.000

P31943 HNRH1 0.018 0.000 Q9ULQ0 FA40B 0.020 100.000

P50991 TCPD 0.017 1.917 P63167 DYL1 0.018 100.000

Q99832 TCPH 0.017 1.533 Q15172 2A5A 0.018 100.000

P35527 K1C9 0.016 0.445 Q5VT06 CE350 0.017 100.000

P62280 RS11 0.016 0.000 P19387 RPB3 0.015 100.000

Q8IXB1 DJC10 0.016 0.000 Q9BRV8 SIKE1 0.015 100.000

P12755 SKI 0.015 0.417 Q14674 ESPL1 0.014 100.000

P35908 K22E 0.015 0.000 Q96N11 CG026 0.008 100.000

P60709 ACTB 0.014 0.536 Q9BXL8 CDCA4 0.008 100.000

P26599 PTBP1 0.014 0.000 P11498 PYC 0.307 2.085

P27708 PYR1 0.014 0.000 P07437 TBB5 0.215 3.657

Q92841 DDX17 0.014 0.000 H11111 His-HA-Strep 0.154 0.446

Q9P2J5 SYLC 0.014 0.000 P68363 TBA1B 0.134 2.871

Q9UMS4 PRP19 0.012 0.000 P11142 HSP7C 0.132 1.012

P00761 TRYP 0.011 0.238 P04350 TBB4 0.131 0.000

61  

Table S4. Inter-protein cross-links identified on a PP2A protein-protein network.

Protein complexes were affinity-purified via the His6-HA-StrepII-tag of 14 bait proteins and

interacting proteins were cross-linked by DSS. The linked peptides were identified by mass

spectrometry and the dedicated search engine xQuest. In total, 35 cross-linking experiments of

14 bait proteins resulted in the identification of 179 inter-protein cross-links. 176 inter-protein

cross-links were mapped onto the PP2A network (uncolored background) and three onto

contaminating proteins (yellow background). The distances spanned by cross-links were

evaluated on available crystal structures and comparative models. For inter-protein cross-links

not unambiguously assigned to either paralog form of the PP2A catalytic, scaffolding or

regulatory subunits, the paralogs were listed according to their spectral counts. The distance

measurements of 14 ambiguously assigned inter-protein cross-links were displayed separately

(paralog with less spectral counts on blue background).

Table S4.1.

(No., Cross-link identifier; Bait, UniProt entry name of bait protein; Topology, amino acid

sequences of peptides indicating the relative position of the linked lysines; Protein1, Protein2,

UniProt entry of cross-linked proteins; Pos1, Pos2, absolute amino acid position of linked

lysines)

No. Bait Topology Protein1 Protein2 Pos1 Pos2

1 FR1OP IKAELR-AEIKR-a2-b4 sp|O95684|FR1OP sp|Q5VT06|CE350 34 1758

2 SGOL1 LAAELNKFMLEK-RIDAQHKR-a7-b7 sp|P05165|PCCA sp|P05166|PCCB 648 60

3 IGBP1 FMLEKVTEDTSSVLR-RIDAQHKR-a5-b7 sp|P05165|PCCA sp|P05166|PCCB 653 60

4 CT2NL LGGKLSSEDK-LFEMAYKK-a4-b7 sp|P11021|GRP78 sp|P38646|GRP75 585 653

5 PP4C MLVDDIGDVTITNDGATILKLLEVEHPAAK-KKGDDQSR-a20-b2

sp|P17987|TCPA sp|P49368|TCPG 63 529

6 PP4C LHPESKDDKHGSYEDAVHSGALND-MIQDGKGDVTITNDGATILK-a6-b6

sp|P17987|TCPA sp|P50991|TCPD 538 65

7 PP4C MLVDDIGDVTITNDGATILKLLEVEHPAAK-IDDIVSGHKK-a20-b9

sp|P17987|TCPA sp|P49368|TCPG 63 527

8 2ABG SQNVMAAASIANIVKSSLGPVGLDK-KVQSGNINAAK-a15-b1

sp|P17987|TCPA sp|P49368|TCPG 33 21

9 2ABG LLEVEHPAAKVLCELADLQDK-KGDDQSR-a10-b1 sp|P17987|TCPA sp|P49368|TCPG 73 529

10 2ABG LHPESKDDKHGSYEDAVHSGALND-IDDIVSGHKK-a9-b9

sp|P17987|TCPA sp|P49368|TCPG 541 527

11 2A5E KLSTIALALGVER-KLEDLELKR-a1-b8 sp|P30153|2AAA sp|Q16537|2A5E 34 456

12 2A5E AVGPEITKTDLVPAFQNLMKDCEAEVR-SQGKPIELTPLPLLK-a20-b4

sp|P30153|2AAA sp|Q16537|2A5E 292 41

13 2A5E KLSTIALALGVER-EREELWKK-a1-b7 sp|P30153|2AAA sp|Q16537|2A5E 34 448

14 2A5E KLSTIALALGVER-KLEDLELKR-a1-b1 sp|P30153|2AAA sp|Q16537|2A5E 34 449

15 2A5G RAAASKLGEFAK-RKSELPQDPHTK-a6-b2 sp|P30153|2AAA sp|Q13362|2A5G 188, 200 496

16 2A5G KLSTIALALGVER-KDRPLAR-a1-b1 sp|P30153|2AAA sp|Q13362|2A5G 34, 46 488

17 2A5G SLQKIGPILDNSTLQSEVKPILEK-IGGKSPDTNYLFMGDYVDR-a4-b4

sp|P30153|2AAA sp|P67775|PP2AA 546 74

18 2A5G SLQKIGPILDNSTLQSEVKPILEK-IGGKSPDTNYLFMGDYVDR-a4-b4

sp|P30153|2AAA sp|P62714|PP2AB 546 74

19 2A5G AISHEHSPSDLEAHFVPLVKR-RKSELPQDPHTK-a20-b2

sp|P30153|2AAA sp|Q13362|2A5G 133 496

20 2A5G FGKEWAHATIIPK-KALEAHCR-a3-b1 sp|P30153|2AAA sp|Q13362|2A5G 475 507

21 2A5G IGPILDNSTLQSEVKPILEKLTQDQDVDVK-KALEAHCR-a20-b1

sp|P30153|2AAA sp|Q13362|2A5G 566 507

22 PP2AA AISHEHSPSDLEAHFVPLVKR-ALEAHKR-a20-b6 sp|P30153|2AAA sp|Q13362|2A5G 133 589

23 PP2AA KLSTIALALGVER-MKEREEMWQK-a1-b2 sp|P30153|2AAA sp|Q14738|2A5D 34 500

24 PP2AA SLQKIGPILDNSTLQSEVKPILEK-VFTKELDQWIEQLNECK-a4-b4

sp|P30153|2AAA sp|P67775|PP2AA 546 8

62  

No. Bait Topology Protein1 Protein2 Pos1 Pos2

25  PP2AB LNSIKKLSTIALALGVER-VAALSKAEER-a6-b6 sp|P30153|2AAA sp|Q13136|LIPA1 34, 46 404

26  PP2AB QAAEDKSWR-FNLSKNR-a6-b5 sp|P30153|2AAA sp|Q14738|2A5D 255 96

27  PP2AB KLSTIALALGVER-LKMKER-a1-b4 sp|P30153|2AAA sp|Q13362|2A5G 34 424

28  2A5G KLSTIALALGVER-RKSELPQDPHTK-a1-b2 sp|P30153|2AAA sp|Q13362|2A5G 34, 46 496

29  2A5G AISHEHSPSDLEAHFVPLVKR-KALEAHCR-a20-b1 sp|P30153|2AAA sp|Q13362|2A5G 133 507

30  2A5G DKAVESLR-KDRPLAR-a2-b1 sp|P30153|2AAA sp|Q13362|2A5G 107, 119 488

31  2A5G AAASHKVK-KALEAHCR-a6-b1 sp|P30153|2AAA sp|Q13362|2A5G 305 507

32  2A5G VSSAVKAELR-KALEAHCR-a6-b1 sp|P30153|2AAA sp|Q13362|2A5G 163 507

33  2A5G LGEFAKVLELDNVK-KSELPQDPHTK-a6-b1 sp|P30153|2AAA sp|Q13362|2A5G 194 496

34  2A5G AISHEHSPSDLEAHFVPLVKR-KDRPLAR-a20-b1 sp|P30153|2AAA sp|Q13362|2A5G 133 488

35  2A5G LNSIKKLSTIALALGVER-VAALSKAEER-a5-b6 sp|P30153|2AAA sp|Q13136|LIPA1 33, 45 404

36  FR1OP KLSTIALALGVER-VKNPNNLDEIK-a1-b2 sp|P30153|2AAA sp|Q5VT06|CE350 34, 46 3013

37  2A5E KLSTIALALGVER-KLEDLELKR-a1-b8 sp|P30154|2AAB sp|Q16537|2A5E 46 456

38  2A5E KLSTIALALGVER-EREELWKK-a1-b7 sp|P30154|2AAB sp|Q16537|2A5E 46 448

39  2A5E KLSTIALALGVER-KLEDLELKR-a1-b1 sp|P30154|2AAB sp|Q16537|2A5E 46 449

40  PP2AA KLSTIALALGVER-MKEREEMWQK-a1-b2 sp|P30154|2AAB sp|Q14738|2A5D 46 500

41  PP2AB QAAEDKSWR-FNLSKNR-a6-b5 sp|P30154|2AAB sp|Q14738|2A5D 267 96

42  PP2AB KLSTIALALGVER-LKMKER-a1-b4 sp|P30154|2AAB sp|Q13362|2A5G 46 424

43  2ABG AGMSSLKG-AVLKPR-a7-b4 sp|P40227|TCPZ sp|Q9Y2T4|2ABG 530 389

44  2ABG TLNPKAEVAR-AVLKPR-a5-b4 sp|P40227|TCPZ sp|Q9Y2T4|2ABG 10 389

45  2ABG AGMSSLKG-KKGDDQSR-a7-b2 sp|P40227|TCPZ sp|P49368|TCPG 530 529

46  PP2AA MLVIEQCKNSR-ENNKPR-a8-b4 sp|P48643|TCPE sp|P63151|2ABA 378 387

47  PP4C IDDIRKPGESEE-KRVPDHHPC-a6-b1 sp|P48643|TCPE sp|P78371|TCPB 535 527

48  PP4C LMGLEALKSHIMAAK-QKIHPTSVISGYR-a8-b2 sp|P48643|TCPE sp|P17987|TCPA 35 111

49  PP4C TTLGSKVVNSCHR-EATKAAR-a6-b4 sp|P48643|TCPE sp|P78371|TCPB 176 135

50  PP4C GGNKMIIEEAKR-KRVPDHHPC-a4-b1 sp|P48643|TCPE sp|P78371|TCPB 392 527

51  2ABG IDDIRKPGESEE-AVLKPR-a6-b4 sp|P48643|TCPE sp|Q9Y2T4|2ABG 535 389

52  2ABG SHIMAAKAVANTMR-GKGAYQDR-a7-b2 sp|P48643|TCPE sp|P50991|TCPD 42 21

53  2ABG IDDIRKPGESEE-ESSKPR-a6-b4 sp|P48643|TCPE sp|Q9Y2T4|2ABG 535 383

54  2ABG LIKGVIVDK-IKIFGSR-a3-b2 sp|P48643|TCPE sp|P78371|TCPB 226 250

55  2ABG MMVDKDGDVTVTNDGATILSMMDVDHQIAK-VDNIIKAAPR-a5-b6

sp|P48643|TCPE sp|P78371|TCPB 64 522

56  2ABG IDDIRKPGESEE-VCVGGKRR-a6-b6 sp|P48643|TCPE sp|Q9Y2T4|2ABG 535 398

57  2ABG IDDIVSGHKK-AGMSSLKG-a9-b7 sp|P49368|TCPG sp|P40227|TCPZ 527 530

58  IGBP1 KVQSGNINAAK-TLNPKAEVAR-a1-b5 sp|P49368|TCPG sp|P40227|TCPZ 21 10

59  PP4C ISIPVDISDSDMMLNIINSSITTKAISR-IITEGFEAAKEK-a24-b10

sp|P49368|TCPG sp|P40227|TCPZ 163 127

60  2ABG KVQSGNINAAK-AAALCDKHSK-a1-b7 sp|P49368|TCPG sp|Q9Y2T4|2ABG 21 260

61  2ABG LQTYKTAVETAVLLLR-YPVNSVNILKAHGR-a5-b10 sp|P49368|TCPG sp|P17987|TCPA 507 199

62  2ABG KVQSGNINAAK-AVLKPR-a1-b4 sp|P49368|TCPG sp|Q9Y2T4|2ABG 21 389

63  2ABG GASKEILSEVER-AGMSSLKG-a4-b7 sp|P49368|TCPG sp|P40227|TCPZ 381 530

64  2ABG KGDDQSR-AVLKPR-a1-b4 sp|P49368|TCPG sp|Q9Y2T4|2ABG 529 389

65  2ABG TCLGPKSMMK-HKPSVKGR-a6-b6 sp|P49368|TCPG sp|P40227|TCPZ 44 430

66  2ABG KVQSGNINAAK-RVCVGGKR-a1-b7 sp|P49368|TCPG sp|Q9Y2T4|2ABG 21 398

67  2ABG KVQSGNINAAK-ESSKPR-a1-b4 sp|P49368|TCPG sp|Q9Y2T4|2ABG 21 383

68  2ABG IDDIVSGHKK-RVCVGGKR-a9-b7 sp|P49368|TCPG sp|Q9Y2T4|2ABG 527 398

69  2ABG EIQVQHPAAKSMIEISR-TLNPKAEVAR-a10-b5 sp|P49368|TCPG sp|P40227|TCPZ 78 10

70  IGBP1 EIQVQHPAAKSMIEISR-AGMSSLKG-a10-b7 sp|P49368|TCPG sp|P40227|TCPZ 78 530

71  IGBP1 KVQSGNINAAK-AGMSSLKG-a1-b7 sp|P49368|TCPG sp|P40227|TCPZ 21 530

72  IGBP1 VEKIPGGIIEDSCVLR-AGMSSLKG-a3-b7 sp|P49368|TCPG sp|P40227|TCPZ 203 530

73  2ABG QITSYGETCPGLEQYAIKK-SKAMTGVEQWPYR-a18-b2

sp|P50990|TCPQ sp|P49368|TCPG 439 427

74  IGBP1 ANEVISKLYAVHQEGNK-WIGLDLSNGKPR-a7-b10 sp|P50990|TCPQ sp|P17987|TCPA 466 494

75  PP4C AVDDGVNTFKVLTR-HKSETDTSLIR-a10-b2 sp|P50990|TCPQ sp|P40227|TCPZ 400 199

76  PP4C APGFAQMLKEGAK-TLNPKAEVAR-a9-b5 sp|P50990|TCPQ sp|P40227|TCPZ 16 10

77  PP4C ALAENSGVKANEVISK-KVQSGNINAAK-a9-b1 sp|P50990|TCPQ sp|P49368|TCPG 459 21

78  PP4C YWAIKLATNAAVTVLR-HKSETDTSLIR-a5-b2 sp|P50990|TCPQ sp|P40227|TCPZ 509 199

79  2ABG EGAKHFSGLEEAVYR-KVQSGNINAAK-a4-b1 sp|P50990|TCPQ sp|P49368|TCPG 20 21

80  2ABG EGAKHFSGLEEAVYR-TLNPKAEVAR-a4-b5 sp|P50990|TCPQ sp|P40227|TCPZ 20 10

81  2ABG MVINHLEKLFVTNDAATILR-LLDVVHPAAKTLVDIAK-a8-b10

sp|P50990|TCPQ sp|Q99832|TCPH 62 77

82  2ABG SILKIDDVVNTR-STLGPKGMDK-a4-b6 sp|P50991|TCPD sp|P78371|TCPB 531 46

83  PP4C LLQKGIHPTIISESFQK-SHIMAAKAVANTMR-a4-b7 sp|P50991|TCPD sp|P48643|TCPE 126 42

84  PP4C GIHPTIISESFQKALEK-STLGPKGMDK-a13-b6 sp|P50991|TCPD sp|P78371|TCPB 139 46

85  PP4C LLQKGIHPTIISESFQK-KIHPQTIIAGWR-a4-b1 sp|P50991|TCPD sp|P78371|TCPB 126 120

86  PP4C GIHPTIISESFQKALEK-QVKEMNPALGIDCLHK-a13-b3 sp|P50991|TCPD sp|P48643|TCPE 139 483

87  2ABG GKGAYQDRDKPAQIR-AVLKPR-a2-b4 sp|P50991|TCPD sp|Q9Y2T4|2ABG 21 389

88  2ABG GKGAYQDRDKPAQIR-EAESLIAKK-a2-b8 sp|P50991|TCPD sp|P78371|TCPB 21 119

89  2ABG GKGAYQDRDKPAQIR-EAVAMESYAKALR-a2-b10 sp|P50991|TCPD sp|P78371|TCPB 21 441

90  2ABG TSLGPKGMDK-LACKEAVR-a6-b4 sp|P50991|TCPD sp|P17987|TCPA 55 126

91  2ABG GKGAYQDRDKPAQIR-KIHPQTIIAGWR-a2-b1 sp|P50991|TCPD sp|P78371|TCPB 21 120

92  2ABG GKGAYQDRDKPAQIR-AVLKPR-a10-b4 sp|P50991|TCPD sp|Q9Y2T4|2ABG 29 389

93  2ABG GKGAYQDRDKPAQIR-VDNIIKAAPR-a10-b6 sp|P50991|TCPD sp|P78371|TCPB 29 522

94  IGBP1 GKGAYQDRDKPAQIR-KRVPDHHPC-a2-b1 sp|P50991|TCPD sp|P78371|TCPB 21 527

95  IGBP1 ESEVKALCAK-QKKELEHR-a5-b3 sp|P60510|PP4C sp|P78318|IGBP1 26 166

96  PP4C ALCAKAR-KELEHR-a5-b1 sp|P60510|PP4C sp|P78318|IGBP1 31 166

97  PP2AB AKEILTKESNVQEVR-YKQKK-a7-b2 sp|P62714|PP2AB sp|P78318|IGBP1 41 163

98  PP2AB AKEILTKESNVQEVR-YKQKK-a2-b2 sp|P62714|PP2AB sp|P78318|IGBP1 36 163

99  PP2AB TLCEKAK-KELEHR-a5-b1 sp|P62714|PP2AB sp|P78318|IGBP1 34 166

63  

No. Bait Topology Protein1 Protein2 Pos1 Pos2

100  SGOL1 CGNQAAIMELDDTLKYSFLQFDPAPR-NLAEIGKR-a15-b7

sp|P62714|PP2AB sp|Q5FBB7|SGOL1 283 35

101  IGBP1 AKEILTKESNVQEVR-KELEHR-a7-b1 sp|P62714|PP2AB,sp|P67775|PP2AA

sp|P78318|IGBP1 41, 41 166

102  IGBP1 AKEILTKESNVQEVR-QKKELEHR-a7-b2 sp|P62714|PP2AB,sp|P67775|PP2AA

sp|P78318|IGBP1 41, 41 165

103  IGBP1 AKEILTKESNVQEVR-QAKIQR-a7-b3 sp|P62714|PP2AB,sp|P67775|PP2AA

sp|P78318|IGBP1 41, 41 158

104  PP2AB HSKLFEEPEDPSNR-QAAEDKSWR-a3-b6 sp|P63151|2ABA sp|P30153|2AAA 267 255

105  PP2AB HSKLFEEPEDPSNR-QAAEDKSWR-a3-b6 sp|P63151|2ABA sp|P30154|2AAB 267 267

106  PP2AB KDEISVDSLDFNKK-KPGRKYER-a1-b5 sp|P63151|2ABA,sp|Q66LE6|2ABD

sp|Q9UL03|INT6 405, 411 826

107  PP2AA KDEISVDSLDFNKK-KPGRKYER-a1-b1 sp|P63151|2ABA,sp|Q66LE6|2ABD

sp|Q9UL03|INT6 405, 411 822

108  CT2NL YNIEKDIAAHIK-AKLNREENR-a5-b2 sp|P63167|DYL1 sp|Q9P2B4|CT2NL 36 252

109  CT2NL YNIEKDIAAHIK-HRMNKHK-a5-b5 sp|P63167|DYL1 sp|Q13033|STRN3 36 280

110  SGOL1 SLCEKAKEILTK-TVPQKK-a7-b5 sp|P67775|PP2AA sp|Q5FBB7|SGOL1 36 323

111  IGBP1 QLSESQVKSLCEKAK-QAKIQR-a8-b3 sp|P67775|PP2AA sp|P78318|IGBP1 29 158

112  2ABG IGGKSPDTNYLFMGDYVDR-FNVAKSLQK-a4-b5 sp|P67775|PP2AA sp|P30153|2AAA 74 542

113  2ABG IGGKSPDTNYLFMGDYVDR-FNVAKSLQK-a4-b5 sp|P67775|PP2AA sp|P30154|2AAB 74 554

114  2A5E EILTKESNVQEVR-SGSLERKVK-a5-b7 sp|P67775|PP2AA,sp|P62714|PP2AB

sp|O94964|CT117 41, 41 1126

115  2A5G EILTKESNVQEVR-KALEAHCR-a5-b1 sp|P67775|PP2AA,sp|P62714|PP2AB

sp|Q13362|2A5G 41, 41 507

116  2A5G EILTKESNVQEVR-KDRPLAR-a5-b1 sp|P67775|PP2AA,sp|P62714|PP2AB

sp|Q13362|2A5G 41, 41 488

117  IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-SLCEKAK-a12-b5 sp|P78318|IGBP1 sp|P67775|PP2AA 306 34

118  IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-ALCAKAR-a1-b5 sp|P78318|IGBP1 sp|P60510|PP4C 295 31

119  PP2AA NMAQAKVFGAGYPSLPTMTVSDWYEQHR-IGGKSPDTNYLFMGDYVDR-a6-b4

sp|P78318|IGBP1 sp|P67775|PP2AA 253 74

120  IGBP1 QKKELEHR-ALCAKAR-a3-b5 sp|P78318|IGBP1 sp|P60510|PP4C 166 31

121  IGBP1 QKKELEHR-SLCEKAK-a3-b5 sp|P78318|IGBP1 sp|P67775|PP2AA 166 34

122  IGBP1 KRVPDHHPC-MIIEEAKR-a1-b7 sp|P78371|TCPB sp|P48643|TCPE 527 399

123  PP2AA KLGGSLADSYLDEGFLLDKK-KTWNPKFTLR-a1-b1 sp|P78371|TCPB sp|Q9NRL3|STRN4 204 426

124  2ABG LTSFIGAIAIGDLVKSTLGPK-DKPAQIR-a15-b2 sp|P78371|TCPB sp|P50991|TCPD 40 29

125  2ABG LTSFIGAIAIGDLVKSTLGPK-GKGAYQDRDKPAQIR-a15-b2

sp|P78371|TCPB sp|P50991|TCPD 40 21

126  2ABG KIHPQTIIAGWR-DKPAQIR-a1-b2 sp|P78371|TCPB sp|P50991|TCPD 120 29

127  2ABG VDNIIKAAPR-GKGAYQDR-a6-b2 sp|P78371|TCPB sp|P50991|TCPD 522 21

128  2ABG VDNIIKAAPR-VCVGGKRR-a6-b6 sp|P78371|TCPB sp|Q9Y2T4|2ABG 522 398

129  2ABG EAESLIAKK-DKPAQIR-a8-b2 sp|P78371|TCPB sp|P50991|TCPD 119 29

130  2ABG KRVPDHHPC-AVLKPR-a1-b4 sp|P78371|TCPB sp|Q9Y2T4|2ABG 527 389

131  SGOL1 VEVTEFEDIKSGYR-NKNLAEIGK-a10-b2 sp|Q01105|SET sp|Q5FBB7|SGOL1 132 28

132  SGOL1 RSSQTQNKASR-NLAEIGKRR-a8-b7 sp|Q01105|SET sp|Q5FBB7|SGOL1 189 35

133  SGOL1 RSSQTQNKASR-NKNLAEIGKR-a8-b2 sp|Q01105|SET sp|Q5FBB7|SGOL1 189 28

134  SGOL1 LRQPFFQKR-MKEKR-a8-b2 sp|Q01105|SET sp|Q5FBB7|SGOL1 83 23

135  PP2AB DAFRKTWNPK-LNSIKK-a5-b5 sp|Q13033|STRN3 sp|P30153|2AAA ,sp|P30154|2AAB

468 33, 45

136  2A5G KALEAHCR-KLVEKFGK-a1-b5 sp|Q13362|2A5G sp|P30153|2AAA 507 472

137  2A5G DEAHQAQKDPK-LGSTKGK-a8-b5 sp|Q13362|2A5G sp|Q9BWN1|PRR14 484 420

138  2A5G EREEAWVKIENLAK-EELQAYKAVR-a8-b7 sp|Q13362|2A5G sp|Q14674|ESPL1 432 593

139  PP2AB DSTLTEPVVMALLKYWPK-KIQSVCLNVSSTLQSK-a14-b1

sp|Q13362|2A5G sp|Q9NVH2|INT7 291 846

140  PP2AB QCCVLFDFVSDPLSDLKWKEVK-KLQKK-a17-b4 sp|Q13362|2A5G sp|Q13136|LIPA1 64 860

141  2A5G RKSELPQDPHTK-SLCEKAK-a2-b5 sp|Q13362|2A5G sp|P67775|PP2AA 496 34

142  2A5G RKSELPQDPHTK-LNSIKK-a2-b5 sp|Q13362|2A5G sp|P30153|2AAA ,sp|P30154|2AAB

496 33, 45

143  2A5G RKSELPQDPHTK-VSSAVKAELR-a2-b6 sp|Q13362|2A5G sp|P30153|2AAA 496 163

144  2A5G KALEAHCR-SLCEKAK-a1-b5 sp|Q13362|2A5G sp|P67775|PP2AA 507 34

145  2A5G KDRPLAR-LNSIKK-a1-b5 sp|Q13362|2A5G sp|P30153|2AAA ,sp|P30154|2AAB

488 33, 45

146  SGOL1 IYGKFLGLR-NKNLAEIGK-a4-b2

sp|Q13362|2A5G,sp|Q14738|2A5D,sp|Q15172|2A5A,sp|Q16537|2A5E

sp|Q5FBB7|SGOL1 192, 268, 217, 209

28

147  PP2AB EKEPPKVAK-VLLGKSR-a2-b5 sp|Q14738|2A5D sp|Q8N201|INT1 9 1683

148  2A5D APPPLPPVYSMETETPTAEDIQLLKR-EILTKESNVQEVR-a25-b5

sp|Q14738|2A5D sp|P67775|PP2AA,sp|P62714|PP2AB

548 41, 41

149  PP2AA APPPLPPVYSMETETPTAEDIQLLKR-KLSTIALALGVER-a25-b1

sp|Q14738|2A5D sp|P30153|2AAA ,sp|P30154|2AAB

548 34, 46

150  SGOL1 GVIVESAYSDIVKMISANIFR-QAAEDKSWR-a13-b6 sp|Q15172|2A5A sp|P30153|2AAA 125 255

151  SGOL1 GVIVESAYSDIVKMISANIFR-QAAEDKSWR-a13-b6 sp|Q15172|2A5A sp|P30154|2AAB 125 267

152  PP4C KQLRAAQLQHSEK-EKEPPK-a1-b2 sp|Q16204|CCDC6 sp|Q14738|2A5D 274 9

153  2A5E KLEDLELKR-LNSIKK-a8-b5 sp|Q16537|2A5E sp|P30153|2AAA 456 33

154  2A5E KLEDLELKR-LNSIKK-a8-b5 sp|Q16537|2A5E sp|P30154|2AAB 456 45

155  2A5E SQGKPIELTPLPLLK-QAAEDKSWR-a4-b6 sp|Q16537|2A5E sp|P30153|2AAA 41 255

156  2A5E SQGKPIELTPLPLLK-QAAEDKSWR-a4-b6 sp|Q16537|2A5E sp|P30154|2AAB 41 267

157  2A5E EELWKKLEDLELK-QLKESKLK-a5-b3 sp|Q16537|2A5E sp|O94988|FA13A 448 720

158  SGOL1 MLVLALENEKSK-SSQTQNKASR-a10-b7 sp|Q5FBB7|SGOL1 sp|Q01105|SET 72 189

159  SGOL1 KSFQDSLEDIK-LRQPFFQKR-a1-b8 sp|Q5FBB7|SGOL1 sp|Q01105|SET 9 83

160  SGOL1 TKEDILESKSEQTK-SSQTQNKASR-a2-b7 sp|Q5FBB7|SGOL1 sp|Q01105|SET 269 189

161  SGOL1 TKEDILESKSEQTK-IYGKFLGLR-a9-b4 sp|Q5FBB7|SGOL1

sp|Q13362|2A5G,sp|Q14738|2A5D,sp|Q15172|2A5A,sp|Q16537|2A5E

276 192, 268, 217, 209

162  SGOL1 TKEDILESKSEQTK-KEKER-a9-b3 sp|Q5FBB7|SGOL1 sp|Q16537|2A5E 276 441

64  

No. Bait Topology Protein1 Protein2 Pos1 Pos2

163  PP2AA LVSSEQALKELGLAEHQLR-RAEVLALPFKR-a9-b10 sp|Q5TA45|INT11 sp|Q9NV88|INT9 500 510

164  2A5G LAKDSIVAQTQKLEDQK-RKSELPQDPHTK-a12-b2 sp|Q5THK1|PR14L sp|Q13362|2A5G 1463 496

165  PP4C YIXKSFLFEPVVK-YMVADKFTELQK-a4-b6 sp|Q6IN85|P4R3A sp|P30153|2AAA 576 266

166  CT2NL RGSDSKPSLSLPRK-LTQQLEFEKSQVK-a6-b9 sp|Q8WZ74|CTTB2 sp|Q9P2B4|CT2NL 276 151

167  CT2NL SFLPVPRSKVTQCSQNTK-HKEIIVK-a9-b2 sp|Q8WZ74|CTTB2 sp|Q9ULQ0|FA40B 1619 567

168  FR1OP NTNEFYKTIPR-VKNPNNLDEIK-a7-b2 sp|Q969Q6|P2R3C sp|Q5VT06|CE350 54 3013

169  PP2AB KPVEAESVEGVVR-NKDIQR-a1-b2 sp|Q96HW7|INT4 sp|Q9NV88|INT9 62 159

170  IGBP1 GKATISNDGATILK-KRVPDHHPC-a2-b1 sp|Q99832|TCPH sp|P78371|TCPB 55 527

171  PP4C QQLLIGAYAKALEIIPR-QKIHPTSVISGYR-a10-b2 sp|Q99832|TCPH sp|P17987|TCPA 440 111

172  2ABG INALTAASEAACLIVSVDETIKNPR-AVLKPR-a22-b4 sp|Q99832|TCPH sp|Q9Y2T4|2ABG 521 389

173  2ABG QVKPYVEEGLHPQIIIR-NADELVKQK-a3-b7 sp|Q99832|TCPH sp|P17987|TCPA 109 109

174  PP2AB RMLLTNNAKNHSPK-KAVKR-a9-b1 sp|Q9H0H0|INT2 sp|Q9NVH2|INT7 750 266

175  PP2AB MLLTNNAKNHSPK-KAVKR-a8-b4 sp|Q9H0H0|INT2 sp|Q9NVH2|INT7 750 269

176  PP2AB EDKEDKSEK-LFIQKLR-a6-b5 sp|Q9NVM9|M89BB

sp|Q13362|2A5G 583 45

177  PP4C NVMVVSCVYPSSEKNNSNSLNR-ALCAKAR-a14-b5 sp|Q9NY27|PP4R2 sp|P60510|PP4C 141 31

178  PP4C NVMVVSCVYPSSEKNNSNSLNR-ESEVKALCAK-a14-b5

sp|Q9NY27|PP4R2 sp|P60510|PP4C 141 26

179  PP4C NVMVVSCVYPSSEKNNSNSLNR-CELIKESEVK-a14-b5 sp|Q9NY27|PP4R2 sp|P60510|PP4C 141 21

180  CT2NL EQKKLSSQLEEER-LLNKLTKWK-a4-b4 sp|Q9P2B4|CT2NL sp|Q9ULQ0|FA40B 163 673

181  CT2NL AKLNREENR-KAVIK-a2-b1 sp|Q9P2B4|CT2NL sp|P63167|DYL1,sp|Q96FJ2|DYL2

252 5, 5

182  CT2NL EQKKLSSQLEEER-FKRWK-a4-b2 sp|Q9P2B4|CT2NL sp|Q9P289|MST4 163 292

183  CT2NL YGKYNISDPLMALQR-RGSDSKPSLSLPRK-a3-b6 sp|Q9P2B4|CT2NL sp|Q8WZ74|CTTB2 47 276

184  CT2NL DLVIEALKAQHR-MLEYALKQER-a8-b7 sp|Q9P2B4|CT2NL sp|Q9NRL3|STRN4,sp|O43815|STRN,sp|Q13033|STRN3

33 126, 110,

126

185  PP2AB KPGRKYER-FRPKDIR-a1-b4 sp|Q9UL03|INT6 sp|Q13136|LIPA1 822 1147

186  2ABG AAALCDKHSKLFEEPEDPSNR-QAAEDKSWR-a10-b6 sp|Q9Y2T4|2ABG sp|P30153|2AAA 263 255

187  2ABG AAALCDKHSKLFEEPEDPSNR-QAAEDKSWR-a10-b6 sp|Q9Y2T4|2ABG sp|P30154|2AAB 263 267

188  2ABG HSKLFEEPEDPSNR-KVQSGNINAAK-a3-b1 sp|Q9Y2T4|2ABG sp|P49368|TCPG 263 21

189  2ABG SFFSEIISSVSDVKFSHSGR-TLNPKAEVAR-a14-b5 sp|Q9Y2T4|2ABG sp|P40227|TCPZ 288 10

190  2ABG AAALCDKHSK-KRVPDHHPC-a7-b1 sp|Q9Y2T4|2ABG sp|P78371|TCPB 260 527

191  2ABG AAALCDKHSK-QAAEDKSWR-a7-b6 sp|Q9Y2T4|2ABG sp|P30153|2AAA 260 255

192  2ABG AAALCDKHSK-QAAEDKSWR-a7-b6 sp|Q9Y2T4|2ABG sp|P30154|2AAB 260 267

193  CT2NL HTLDGAACLLNSNKYFPSR-KNAALDVEPIHAFR-a14-b1

sp|Q9Y3A3|MOBL3 sp|Q9NRL3|STRN4 140 475

65  

Table S4.2.

(No., cross-link identifier; N_Id, number of fragment ion spectra assigned to the cross-link in

entire dataset; N_Exp, number of experiments identifying the cross-link; m/z, mass to charge

ratio; z, charge; Error, mass deviation from the monoisotopic precursor mass in ppm; Tic,

relative contribution to total ion current; Id-Score, xQuest identification score; X ions,

minimum number of cross-link ions per peptide and cross-link; PDB, PDB entry of protein

structure for evaluation of cross-link distances; Euclidean, Euclidean cross-link distance

measured in PDB structure or comparative model in Å; SAS, solvent-accessible surface

(SAS) cross-link distance measured in PDB structure or comparative model in Å; TRiC,

indicating whether shortest cross-link distance mapped within a heterooctameric TRiC ring or

between rings)

No. N_Id N_Exp m/z z Error [ppm] Tic Id-score X ions PDBEuclidean

[Å] SAS [Å]

TRiC

1 2 1 494.972 3 -0.8 0.57 34.76 2

2 81 13 514.291 5 3.2 0.63 34.03 4

3 6 5 729.642 4 1.6 0.58 33.19 4

4 2 1 550.798 4 5.4 0.24 30.35 4

5 6 5 853.255 5 5.1 0.54 28.15 3 TRiC 14.1 33.4 intra-ring

6 1 1 970.475 5 3.7 0.47 27.83 6 TRiC 10.1 13.2 intra-ring

7 3 2 888.882 5 4.4 0.63 27.39 3 TRiC 17.1 26.5 intra-ring

8 12 5 1246.348 3 0.2 0.67 35.37 7 TRiC 15.3 22.7 intra-ring

9 2 2 667.545 5 -1.6 0.45 31.80 2 TRiC 20.1 45.6 intra-ring

10 1 1 774.778 5 0.3 0.35 26.01 5 TRiC 17.4 23.6 intra-ring

11 24 4 884.532 3 3.9 0.59 37.27 6 3fga 18.1 22.9

12 6 3 1201.406 4 5.4 0.38 36.74 7 3fga 42.5 51.6

13 2 2 875.841 3 4.1 0.39 34.67 5 3fga 10.9 17.8

14 13 2 531.122 5 2.8 0.63 34.55 4 3fga 10.8 27.6

15 10 2 565.114 5 1.7 0.58 37.15 5

16 15 4 591.61 4 0.9 0.61 33.50 1

17 16 8 1234.654 4 4.6 0.50 32.73 4 3fga 18 18.1

18 1234.654 4 4.6 0.50 32.73 4 3fga 17.4 21.2

19 4 2 789.218 5 -1.3 0.61 31.31 3

20 1 1 524.684 5 -0.2 0.25 31.24 3

21 2 2 892.282 5 4.2 0.53 28.34 3

22 3 2 833.454 4 6.3 0.52 30.81 3

23 3 2 968.195 3 5.1 0.45 30.72 6 3fga 15.5 22.7

24 6 3 1242.667 4 2.7 0.40 29.85 3 3fga 19.5 21.8

25  28 6 784.961 4 -3.2 0.39 32.29 5

26  9 3 527.275 4 1.3 0.19 33.40 4 3fga 42.8 54.4

27  8 3 771.463 3 -0.2 0.62 29.76 2 3fga 15.2 22.7

28  14 3 736.673 4 1.9 0.66 35.04 3

29  11 2 698.966 5 -0.5 0.39 34.20 4

30  4 1 637.367 3 1.7 0.47 33.13 4

31  3 1 645.022 3 2.6 0.32 32.53 3

32  2 1 546.051 4 0 0.42 32.23 2

33  3 1 599.13 5 4.3 0.40 31.75 2

34  3 1 673.172 5 4.6 0.58 29.78 3

35  1 1 784.964 4 0.7 0.28 28.71 2

36  1 1 698.654 4 -1 0.48 30.56 2

37  884.532 3 3.9 0.59 37.27 6 3fga 16.5 22.9

38  875.841 3 4.1 0.39 34.67 5 3fga 10.3 18.6

39  531.122 5 2.8 0.63 34.55 4 3fga 9.6 27.2

40  968.195 3 5.1 0.45 30.72 6 3fga 16.5 24.5

41  527.275 4 1.3 0.19 33.40 4 3fga 42 55.6

42  771.463 3 -0.2 0.62 29.76 2 3fga 16 23.6

43  2 1 524.304 3 -1.6 0.53 38.77 4

44  6 1 480.54 4 -4 0.64 38.48 3

45  3 1 607.643 3 -2.4 0.53 30.66 3 TRiC 30.8 39.3 intra-ring

46  1 1 568.798 4 6.3 0.50 29.96 4

47  32 11 534.865 5 -0.8 0.52 35.59 5 TRiC 27 35.1 intra-ring

48  16 6 647.963 5 3.5 0.36 34.67 6 TRiC 26.6 34.1 inter-ring

49  41 10 781.416 3 2.6 0.43 34.29 4 TRiC 25.3 28.8 intra-ring

66  

No. N_Id N_Exp m/z z Error [ppm] Tic Id-score X ions PDBEuclidean

[Å] SAS [Å]

TRiC

50  19 8 657.842 4 -2 0.51 32.91 5 TRiC 21.8 23 intra-ring

51  3 2 552.802 4 -2.2 0.71 36.82 4

52  10 5 633.825 4 -2 0.43 35.77 4 TRiC 25.4 29.3 inter-ring

53  1 1 743.373 3 0 0.23 26.01 4

54  13 5 486.307 4 -2.2 0.72 44.52 5 TRiC 46.4 52.9 intra-ring

55  4 2 1121.815 4 3.7 0.44 36.15 6 TRiC 13.1 26.8 intra-ring

56  2 2 614.818 4 -3.6 0.63 32.32 2

57  1 1 667.027 3 5.3 0.47 25.25 3 TRiC 29.7 40.4 intra-ring

58  20 8 592.089 4 4.4 0.51 38.93 6 TRiC 25.3 30.7 intra-ring

59  3 2 1127.602 4 6.4 0.49 29.46 8 TRiC 19.8 23.4 intra-ring

60  2 2 789.751 3 -3.5 0.39 30.28 6

61  2 1 881.755 4 -0.8 0.53 29.93 5 TRiC 23.1 39.4 intra-ring

62  8 3 488.292 4 -3.2 0.38 38.36 5

63  8 3 735.721 3 2.3 0.47 37.13 6 TRiC 31.9 51.1 intra-ring

64  2 1 407.229 4 -3.2 0.76 34.41 2

65  28 9 440.438 5 -0.6 0.61 34.14 2 TRiC 16.9 19.4 intra-ring

66  7 2 440.449 5 -2.2 0.48 31.91 2

67  4 1 657.36 3 -1.1 0.25 28.85 4

68  1 1 545.804 4 -2.1 0.62 28.79 3

69  2 1 793.935 4 0.3 0.64 28.63 3 TRiC 19.3 40.6 intra-ring

70  19 12 942.163 3 1.5 0.44 34.68 5 TRiC 29.9 51.5 intra-ring

71  4 3 673.03 3 0.3 0.46 29.81 3 TRiC 36.6 42.3 intra-ring

72  4 3 891.476 3 4.3 0.44 27.48 4 TRiC 37 57.5 intra-ring

73  3 1 1292.646 3 5.8 0.50 25.41 5 TRiC 14.6 16.1 inter-ring

74  38 9 679.368 5 3.3 0.55 38.43 8 TRiC 14.7 16.2 inter-ring

75  35 9 986.859 3 2.3 0.59 37.56 7 TRiC 20.4 22.6 intra-ring

76  4 3 646.608 4 3.9 0.58 33.18 5 TRiC 19.6 21.6 inter-ring

77  1 1 724.901 4 2.5 0.28 26.89 1 TRiC 23.5 29.2 inter-ring

78  1 1 643.56 5 1.9 0.26 26.78 4 TRiC 19.8 22.3 intra-ring

79  5 4 740.636 4 -2.8 0.30 29.88 3 TRiC 37.5 40.8 inter-ring

80  1 1 586.51 5 -0.6 0.41 31.00 3 TRiC 20.6 22.5 inter-ring

81  2 2 707.239 6 -1.7 0.39 29.83 2 TRiC 19 22.2 inter-ring

82  2 2 848.466 3 3.3 0.55 35.30 4 TRiC 9.5 12.6 intra-ring

83  23 8 716.198 5 4.9 0.57 37.87 7 TRiC 18 19.4 inter-ring

84  2 1 767.915 4 1.1 0.69 36.33 7 TRiC 15 18.6 intra-ring

85  5 3 700.004 5 1.4 0.40 30.90 1 TRiC 17.3 19 inter-ring

86  7 4 778.419 5 6.5 0.25 30.16 5 TRiC 25.1 28.9 inter-ring

87  8 2 421.408 6 -3.3 0.76 34.25 5

88  28 9 707.886 4 -2.4 0.61 31.19 2 TRiC 15.6 16.9 intra-ring

89  2 2 820.429 4 -1.5 0.67 26.23 3 TRiC 20.7 27.1 intra-ring

90  58 12 706.374 3 -1.6 0.73 41.93 6 TRiC 25.5 28.6 intra-ring

91  47 9 466.546 7 -1 0.58 40.18 8 TRiC 13.9 15.6 intra-ring

92  1 1 421.408 6 -2.3 0.66 33.85 4

93  2 2 588.128 5 -0.1 0.53 28.68 3 TRiC 27.3 29.6 inter-ring

94  9 6 597.911 5 1 0.35 33.95 7 TRiC 33.5 40.3 inter-ring

95  3 2 585.566 4 0.1 0.25 30.39 2

96  21 5 435.241 4 -1.8 0.82 41.47 4

97  73 7 644.62 4 3.4 0.54 38.27 4

98  1 1 859.158 3 4.4 0.32 32.84 5

99  16 4 599.989 3 -1 0.65 37.70 4

100  1 1 1010.263 4 4.6 0.52 30.71 5

101  12 3 673.874 4 3.1 0.47 38.73 3

102  1 1 590.53 5 1.1 0.23 28.99 2

103  3 2 525.702 5 2 0.14 28.66 5

104  43 8 583.283 5 1.2 0.54 32.99 3 3dw8 17.5 19.5

105  583.283 5 1.2 0.54 32.99 3 3dw8 17.3 21.8

106  46 5 702.882 4 5.5 0.32 28.44 4

107  9 3 468.922 6 2 0.38 28.43 2

108  1 1 537.093 5 -0.7 0.39 35.37 5

109  2 1 626.345 4 7 0.27 28.04 3

110  2 2 565.077 4 0.7 0.62 30.94 4

111  1 1 523.893 5 5.6 0.22 29.12 6

112  7 3 1107.224 3 -2.9 0.48 32.89 5 3fga 14.3 16.3

113  1107.224 3 -2.9 0.48 32.89 5 3fga 14.9 17.2

114  2 1 895.834 3 2.5 0.49 28.69 4

115  6 2 889.471 3 1.2 0.38 36.26 6

116  2 1 635.108 4 0.7 0.32 29.76 3

117  3 3 760.758 5 0.1 0.57 32.25 5

118  1 1 751.562 5 3.9 0.49 26.33 5

119  1 1 1094.72 5 0.2 0.51 29.89 0

120  23 5 499.28 4 0 0.42 36.51 5

121  15 5 510.778 4 -1.3 0.75 36.28 3

122  21 8 568.8 4 4 0.76 35.65 4 TRiC 28.6 36.1 intra-ring

123  1 1 600.328 6 -2.8 0.32 28.62 4

124  15 5 1022.594 3 1.3 0.68 33.40 3 TRiC 12 32.9 intra-ring

125  1 1 657.702 6 -3 0.66 29.60 2 TRiC 11.1 26.3 intra-ring

126  58 9 477.677 5 -2.1 0.78 41.91 3 TRiC 19.4 25.3 inter-ring

127  22 7 532.793 4 -0.5 0.55 40.21 5 TRiC 34.6 42 inter-ring

67  

No. N_Id N_Exp m/z z Error [ppm] Tic Id-score X ions PDBEuclidean

[Å] SAS [Å]

TRiC

128  2 2 542.063 4 -3 0.55 33.59 5

129  10 4 651.704 3 -2.7 0.48 33.40 4 TRiC 19.5 24.5 inter-ring

130  3 2 394.022 5 -2 0.71 29.10 3

131  2 2 699.619 4 1.5 0.54 35.14 3

132  1 1 614.842 4 0.7 0.31 30.21 5

133  2 2 636.352 4 0.6 0.40 30.15 2

134  5 1 512.797 4 2 0.21 29.14 4

135  4 1 701.402 3 6.7 0.37 29.49 5

136  9 2 414.837 5 0.8 0.53 36.97 3

137  2 1 698.697 3 -3.7 0.37 28.80 4

138  2 1 612.533 5 3.8 0.39 28.48 3

139  3 2 1005.792 4 0.5 0.72 28.04 5

140  1 1 874.471 4 4.6 0.46 29.98 4

141  26 4 602.822 4 1.1 0.65 41.78 6

142  18 2 455.861 5 -1.4 0.49 37.02 5

143  4 1 658.867 4 1.6 0.50 36.28 6

144  1 1 490.006 4 0 0.73 35.76 5

145  7 3 424.513 4 -0.5 0.60 32.37 2

146  2 1 548.323 4 2 0.50 35.97 3

147  1 1 484.549 4 5.2 0.42 27.91 4

148  1 1 1144.604 4 0.7 0.35 26.80 3

149  3 3 1101.108 4 1.9 0.53 31.41 1

150  6 3 885.715 4 4.4 0.60 34.13 4 3fga 17.8 19.2

151  885.715 4 4.4 0.60 34.13 4 3fga 17.4 19.8

152  1 1 481.07 5 -0.7 0.29 26.61 5

153  14 3 496.552 4 -0.3 0.39 32.20 5 3fga 20.5 25.1

154  496.552 4 -0.3 0.39 32.20 5 3fga 18.3 23.5

155  9 3 716.154 4 4.8 0.32 31.34 5 3fga 38.8 44.9

156  716.154 4 4.8 0.32 31.34 5 3fga 38.3 45.2

157  1 1 557.521 5 -2.3 0.27 30.70 5

158  7 2 655.352 4 0.9 0.60 39.06 4

159  5 2 534.093 5 1 0.43 33.17 4

160  1 1 720.623 4 2.7 0.37 31.16 3

161  2 1 710.643 4 0.7 0.43 34.40 8

162  2 2 616.329 4 -2.2 0.44 31.13 3

163  11 4 593.843 6 -0.1 0.75 41.58 6

164  6 2 872.723 4 -2.5 0.49 28.05 5

165  1 1 807.427 4 1 0.34 22.48 4

166  3 2 649.361 5 0.1 0.32 29.52 4

167  1 1 616.949 5 6.5 0.60 29.27 3

168  1 1 701.622 4 0.1 0.40 33.76 5

169  25 6 578.068 4 0.5 0.52 37.13 3

170  40 13 668.608 4 3.5 0.46 32.29 3 TRiC 32 37 intra-ring

171  16 5 704.81 5 4.4 0.35 32.87 4 TRiC 11.9 26.4 inter-ring

172  10 3 869.985 4 0.5 0.66 34.50 4

173  5 2 800.95 4 3 0.17 28.09 3 TRiC 19 20.9 inter-ring

174  3 2 473.276 5 -0.5 0.25 30.68 2

175  1 1 552.318 4 0.2 0.45 29.93 3

176  1 1 541.301 4 5.2 0.67 27.71 4

177  9 2 1142.236 3 4.3 0.71 36.73 4

178  6 2 943.216 4 5.8 0.72 31.69 1

179  3 2 1290.637 3 5.6 0.71 31.06 6

180  18 2 721.909 4 -1.3 0.29 33.32 5

181  4 2 457.022 4 -0.9 0.37 30.19 2

182  4 2 627.093 4 1.5 0.36 31.21 3

183  1 1 687.571 5 -1.2 0.65 29.69 4

184  1 1 703.387 4 0.4 0.53 27.39 4

185  2 1 526.305 4 -1.1 0.18 27.77 5

186  3 3 729.155 5 4.2 0.27 23.17 3 3fga 17.1 19.4

187  3 3 729.155 5 4.2 0.27 23.17 3 3dw8 17 18.8

188  1 1 738.626 4 -2.6 0.43 30.10 5

189  5 2 863.704 4 1.8 0.78 36.94 5

190  3 1 596.548 4 -3 0.39 32.49 4

191  2 1 582.79 4 -2.5 0.24 28.43 2 3dw8 11.3 13.7

192  582.79 4 -2.5 0.24 28.43 2 3dw8 10.7 13

193  2 1 777.204 5 2.7 0.61 27.87 4

68  

Table S5. Intra-protein cross-links identified on a PP2A protein-protein network.

Affinity-purified protein complexes were cross-linked with DSS and the linked peptides were

identified by mass spectrometry and the search engine xQuest. 35 cross-linking experiments

of 14 His6-HA-StrepII-tagged bait proteins yielded 727 intra-protein cross-links. 570 intra-

protein cross-links were identified on the PP2A network, of these, 347 were mapped on prey

proteins (uncolored background) and 223 on bait proteins (grey background). 157 intra-

protein cross-links were found on contaminating proteins (yellow background). As described

in table S4, the cross-link distances were evaluated on available crystal structures and

comparative models and cross-links which were not unambiguously assigned to a paralog of

the PP2A catalytic, scaffolding or regulatory subunits were displayed separately (blue

background).

Table S5.1.

(No., cross-link identifier; Bait, UniProt entry name of bait protein; Topology, amino acid

sequences of peptides indicating the relative position of the linked lysines; Protein1, Protein2,

UniProt entry of cross-linked proteins; Pos1, Pos2, absolute amino acid position of linked

lysines; ∆aa, number of amino acids separating the linked lysines )

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

1 CT2NL KSTSLDVEPIYTFR-TWNPKFTLR-a1-b5 sp|O43815|STRN sp|O43815|STRN 500 456 44

2 CT2NL CYIASAGADALAKVFV-KTWNPK-a13-b1 sp|O43815|STRN sp|O43815|STRN 777 451 326

3 CT2NL KGQENLK-KDLVRR-a1-b1 sp|O43815|STRN, sp|Q13033|STRN3

sp|O43815|STRN, sp|Q13033|STRN3

89, 105 96, 112 7

4 FR1OP SSLHLLSHETKIGSFLSNR-IKAELR-a11-b2 sp|O95684|FR1OP sp|O95684|FR1OP 225 34 191

5 FR1OP SGLSSLAGAPSLKDSESK-DLKLISDK-a13-b3 sp|O95684|FR1OP sp|O95684|FR1OP 303 318 15

6 FR1OP SKSSLHLLSHETK-TLDGKDK-a2-b5 sp|O95684|FR1OP sp|O95684|FR1OP 214 238 24

7 FR1OP RGNTVLKDLK-IKAELR-a7-b2 sp|O95684|FR1OP sp|O95684|FR1OP 315 34 281

8 FR1OP SKSSLHLLSHETK-IKAELR-a2-b2 sp|O95684|FR1OP sp|O95684|FR1OP 214 34 180

9 FR1OP AAVFLALEEQEKVENK-IKAELR-a12-b2 sp|O95684|FR1OP sp|O95684|FR1OP 50 34 16

10 FR1OP TLDGKDK-IKAELR-a5-b2 sp|O95684|FR1OP sp|O95684|FR1OP 238 34 204

11 FR1OP SSLHLLSHETKIGSFLSNR-TLDGKDK-a11-b5 sp|O95684|FR1OP sp|O95684|FR1OP 225 238 13

12 FR1OP KQAGSLASLSDAPPLK-GNTVLKDLK-a1-b6 sp|O95684|FR1OP sp|O95684|FR1OP 275 315 40

13 FR1OP VENKTPLVNESLKK-IKAELR-a4-b2 sp|O95684|FR1OP sp|O95684|FR1OP 54 34 20

14 FR1OP SKSSLHLLSHETK-DSESKR-a2-b5 sp|O95684|FR1OP sp|O95684|FR1OP 214 308 94

15 FR1OP KANDEANQSDTSVSLSEPK-KFLNTK-a1-b1 sp|O95684|FR1OP sp|O95684|FR1OP 194 64 130

16 FR1OP KANDEANQSDTSVSLSEPK-SPEGKTSAQTTPSK-a1-b5 sp|O95684|FR1OP sp|O95684|FR1OP 194 164 30

17 FR1OP KQAGSLASLSDAPPLK-IKAELR-a1-b2 sp|O95684|FR1OP sp|O95684|FR1OP 275 34 241

18 FR1OP KANDEANQSDTSVSLSEPKSK-SSLHLLSHETKIGSFLSNR-a19-b11 sp|O95684|FR1OP sp|O95684|FR1OP 212 225 13

19 FR1OP AAVFLALEEQEKVENK-KFLNTK-a12-b1 sp|O95684|FR1OP sp|O95684|FR1OP 50 64 14

20 FR1OP KQAGSLASLSDAPPLKSGLSSLAGAPSLK-GNTVLKDLK-a16-b6 sp|O95684|FR1OP sp|O95684|FR1OP 290 315 25

21 FR1OP SPEGKTSAQTTPSK-SKSSLHLLSHETK-a5-b2 sp|O95684|FR1OP sp|O95684|FR1OP 164 214 50

22 FR1OP SGLSSLAGAPSLKDSESK-KQAGSLASLSDAPPLK-a13-b1 sp|O95684|FR1OP sp|O95684|FR1OP 303 275 28

23 FR1OP SKSSLHLLSHETK-KFLNTK-a2-b1 sp|O95684|FR1OP sp|O95684|FR1OP 214 64 150

24 FR1OP SPEGKTSAQTTPSK-KFLNTK-a5-b1 sp|O95684|FR1OP sp|O95684|FR1OP 164 64 100

25 FR1OP KANDEANQSDTSVSLSEPK-SKSSLHLLSHETK-a1-b2 sp|O95684|FR1OP sp|O95684|FR1OP 194 214 20

26 FR1OP LISDKIGSLGLGTGEDDDYVDDFNSTSHR-GNTVLKDLK-a5-b6 sp|O95684|FR1OP sp|O95684|FR1OP 323 315 8

27 FR1OP TSAQTTPSKIPR-IKAELR-a9-b2 sp|O95684|FR1OP sp|O95684|FR1OP 173 34 139

28 FR1OP KFLNTKDGR-IKAELR-a6-b2 sp|O95684|FR1OP sp|O95684|FR1OP 69 34 35

29 FR1OP SPEGKTSAQTTPSK-TLDGKDK-a5-b5 sp|O95684|FR1OP sp|O95684|FR1OP 164 238 74

30 FR1OP LISDKIGSLGLGTGEDDDYVDDFNSTSHRSEK-IKAELR-a5-b2 sp|O95684|FR1OP sp|O95684|FR1OP 323 34 289

31 FR1OP VENKTPLVNESLKK-IKAELR-a13-b2 sp|O95684|FR1OP sp|O95684|FR1OP 63 34 29

32 FR1OP EKGPTTGEGALDLSDVHSPPK-CQQKEK-a2-b4 sp|O95684|FR1OP sp|O95684|FR1OP 140 138 2

33 FR1OP KQAGSLASLSDAPPLK-KFLNTK-a1-b1 sp|O95684|FR1OP sp|O95684|FR1OP 275 64 211

34 FR1OP EKGPTTGEGALDLSDVHSPPK-IKAELR-a2-b2 sp|O95684|FR1OP sp|O95684|FR1OP 140 34 106

69  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

35 FR1OP SSLHLLSHETKIGSFLSNR-SKSSLHLLSHETK-a11-b2 sp|O95684|FR1OP sp|O95684|FR1OP 225 214 11

36 FR1OP EKGPTTGEGALDLSDVHSPPK-FLNTKDGR-a2-b5 sp|O95684|FR1OP sp|O95684|FR1OP 140 69 71

37 FR1OP EKGPTTGEGALDLSDVHSPPK-SPEGKTSAQTTPSK-a2-b5 sp|O95684|FR1OP sp|O95684|FR1OP 140 164 24

38 FR1OP SSLHLLSHETKIGSFLSNR-KQAGSLASLSDAPPLK-a11-b1 sp|O95684|FR1OP sp|O95684|FR1OP 225 275 50

39 CT2NL IKFLVIALK-VVKYER-a2-b3 sp|O95819|M4K4 sp|O95819|M4K5 1035 1030 5

40 CT2NL LENAVKKPEDKK-SSSKSEGSPSQR-a6-b4 sp|O95819|M4K4 sp|O95819|M4K5 725 711 14

41 PP2AB TFDKILVANR-HKQADIR-a4-b2 sp|P05165|PCCA sp|P05165|PCCA 65 385 320

42 2A5E HIEIQVLGDKHGNALWLNER-VAKGYPLR-a10-b3 sp|P05165|PCCA sp|P05165|PCCA 278 378 100

43 2A5E NLGSVGYDPNEKTFDK-VAKGYPLR-a12-b3 sp|P05165|PCCA sp|P05165|PCCA 61 378 317

44 2A5E EAGGNMSIQFLGTVYKVNILTR-VYAEDPYKSFGLPSIGR-a16-b8 sp|P05165|PCCA sp|P05165|PCCA 635 407 228

45 2AAB MPVIKPDIANWELSVKLHDK-LAAELNKFMLEK-a16-b7 sp|P05165|PCCA sp|P05165|PCCA 564 648 84

46 2AAB GDISTKFLSDVYPDGFK-ASAGGGGKGMR-a6-b8 sp|P05165|PCCA sp|P05165|PCCA 502 227 275

47 SGOL1 LITYGSDRTEALKR-FVKGDISTK-a13-b3 sp|P05165|PCCA sp|P05165|PCCA 464 496 32

48 SGOL1 AQAVHPGYGFLSENKEFAR-ASAGGGGKGMR-a15-b8 sp|P05165|PCCA sp|P05165|PCCA 150 227 77

49 SGOL1 KNFYFLEMNTR-FVKGDISTK-a1-b3 sp|P05165|PCCA sp|P05165|PCCA 343 496 153

50 SGOL1 YSSAGTVEFLVDSKK-LLIEKFIDNPR-a14-b5 sp|P05165|PCCA sp|P05165|PCCA 342 262 80

51 SGOL1 KAEVNTIPGFDGVVKDAEEAVR-AVKYSSAGTVEFLVDSKK-a1-b3 sp|P05165|PCCA sp|P05165|PCCA 186 328 142

52 SGOL1 VAKGYPLR-HKQADIR-a3-b2 sp|P05165|PCCA sp|P05165|PCCA 378 385 7

53 SGOL1 CLAAEDVVFIGPDTHAIQAMGDKIESK-ASAGGGGKGMR-a23-b8 sp|P05165|PCCA sp|P05165|PCCA 177 227 50

54 2A5E AYNMVDIIHSVVDEREFFEIMPNYAKNIIVGFAR-TVGIVGNQPKVASGCLDINSSVK-a26-b10

sp|P05166|PCCB sp|P05166|PCCB 338 360 22

55 SGOL1 GAVEIIFKGHENVEAAQAEYIEK-CADFGMAADKNKFPGDSVVTGR-a8-b12 sp|P05166|PCCB sp|P05166|PCCB 474 101 373

56 IGBP1 GAVEIIFKGHENVEAAQAEYIEK-CADFGMAADKNKFPGDSVVTGR-a8-b10 sp|P05166|PCCB sp|P05166|PCCB 474 99 375

57 IGBP1 RIDAQHKR-GKLTAR-a7-b2 sp|P05166|PCCB sp|P05166|PCCB 60 63 3

58 IGBP1 IDAQHKR-IENKRR-a6-b4 sp|P05166|PCCB sp|P05166|PCCB 60 42 18

59 IGBP1 ISVYYNEATGGKYVPR-KLAVNMVPFPR-a12-b1 sp|P07437|TBB5 sp|P07437|TBB5 58 252 194

60 2AAB HWPFQVINDGDKPK-KFGDPVVQSDMK-a12-b1 sp|P08107|HSP71 sp|P08107|HSP71 100 77 23

61 2AAB LIGDAAKNQVALNPQNTVFDAKR-DISQNKR-a7-b6 sp|P08107|HSP71 sp|P08107|HSP71 56 257 201

62 2AAB QATKDAGVIAGLNVLR-LSKEEIER-a4-b3 sp|P08107|HSP71 sp|P08107|HSP71 159 512 353

63 2AAB LVNHFVEEFKRK-HKKDISQNK-a10-b3 sp|P08107|HSP71 sp|P08107|HSP71 246 251 5

64 PP4C ITITNDKGR-LSKEEIER-a7-b3 sp|P08107|HSP71 sp|P08107|HSP71 507 512 5

65 PP4C MVQEAEKYKAEDEVQR-TGKGER-a9-b3 sp|P08107|HSP71 sp|P08107|HSP71 526 190 336

66 PP4C GRLSKEEIER-ISEADKK-a5-b6 sp|P08107|HSP71 sp|P08107|HSP71 512 567 55

67 2ABG STLEPVEKALR-DAKLDK-a8-b3 sp|P08107|HSP71 sp|P08107|HSP71 319 325 6

68 2ABG VSAKNALESYAFNMK-AMTKDNNLLGR-a4-b4 sp|P08107|HSP71 sp|P08107|HSP71 539 451 88

69 2ABG MVQEAEKYKAEDEVQR-TGKGER-a7-b3 sp|P08107|HSP71 sp|P08107|HSP71 524 190 334

70 2ABG LSKEEIER-TGKGER-a3-b3 sp|P08107|HSP71 sp|P08107|HSP71 512 190 322

71 FR1OP LSKEEIER-DISQNKR-a3-b6 sp|P08107|HSP71 sp|P08107|HSP71 512 257 255

72 PP2AB TLLIKTVETR-KLLEGEESR-a5-b1 sp|P08670|VIME sp|P08670|VIME 445 402 43

73 PP2AB TNEKVELQELNDR-FANYIDKVR-a4-b7 sp|P08670|VIME sp|P08670|VIME 104 120 16

74 PP2AB ETNLDSLPLVDTHSKR-TLLIKTVETR-a15-b5 sp|P08670|VIME sp|P08670|VIME 439 445 6

75 PP2AB ETNLDSLPLVDTHSKR-KLLEGEESR-a15-b1 sp|P08670|VIME sp|P08670|VIME 439 402 37

76 2ABG SIDLKDK-YKNIGAK-a5-b2 sp|P10809|CH60 sp|P10809|CH61 87 91 4

77 2ABG GVMLAVDAVIAELKK-KGVITVK-a14-b1 sp|P10809|CH60 sp|P10809|CH61 156 196 40

78 IGBP1 AVQKLRR-EVEKAKR-a4-b4 sp|P11021|GRP78 sp|P11021|GRP78 287 294 7

79 2AAB MVNHFIAEFKRK-HKKDISENK-a10-b3 sp|P11142|HSP7C sp|P11142|HSP7C 246 251 5

80 2AAB LIGDAAKNQVAMNPTNTVFDAKR-DISENKR-a7-b6 sp|P11142|HSP7C sp|P11142|HSP7C 56 257 201

81 2AAB QATKDAGTIAGLNVLR-MVQEAEKYKAEDEK-a4-b9 sp|P11142|HSP7C sp|P11142|HSP7C 159 526 367

82 FA40B ENKITITNDKGR-LSKEDIER-a10-b3 sp|P11142|HSP7C sp|P11142|HSP7C 507 512 5

83 2ABG GTLDPVEKALR-DAKLDK-a8-b3 sp|P11142|HSP7C sp|P11142|HSP7C 319 325 6

84 2ABG ITITNDKGR-TGKGER-a7-b3 sp|P11142|HSP7C sp|P11142|HSP7C 507 190 317

85 2ABG LSKEDIER-KVGAER-a3-b1 sp|P11142|HSP7C sp|P11142|HSP7C 512 188 324

86 FR1OP ITITNDKGR-LSKEDIER-a7-b3 sp|P11142|HSP7C sp|P11142|HSP7C 507 512 5

87 2AAB ILKEDILNYLEK-KTLATPAVR-a3-b1 sp|P11182|ODB2 sp|P11182|ODB2 202 170 32

88 SGOL1 GIKLSFMPFFLK-LREELKPIAFAR-a3-b6 sp|P11182|ODB2 sp|P11182|ODB2 304 295 9

89 SGOL1 LSEVVGSGKDGR-KTLATPAVR-a9-b1 sp|P11182|ODB2 sp|P11182|ODB2 196 170 26

90 PP2AB RLEYKPIK-KVMVANR-a5-b1 sp|P11498|PYC sp|P11498|PYC 35 39 4

91 2A5E VAKENNVDAVHPGYGFLSER-KMGDKVEAR-a3-b1 sp|P11498|PYC sp|P11498|PYC 107 148 41

92 2A5E QKADEAYLIGR-KVHVTK-a2-b1 sp|P11498|PYC sp|P11498|PYC 79 1159 1080

93 2A5E SILVKDTQAMKEMHFHPK-KVHVTK-a11-b1 sp|P11498|PYC sp|P11498|PYC 1096 1159 63

94 2A5E GLAPVQAYLHIPDIIKVAK-QKADEAYLIGR-a16-b2 sp|P11498|PYC sp|P11498|PYC 104 79 25

95 2AAB VIDIKVVAGAK-VLKDLPR-a5-b3 sp|P11498|PYC sp|P11498|PYC 1124 969 155

96 2AAB RLEYKPIKK-KVHVTK-a8-b1 sp|P11498|PYC sp|P11498|PYC 38 1159 1121

97 2AAB QKADEAYLIGR-VIDIKVVAGAK-a2-b5 sp|P11498|PYC sp|P11498|PYC 79 1124 1045

98 2AAB KMGDKVEAR-RLEYKPIKK-a1-b5 sp|P11498|PYC sp|P11498|PYC 148 35 113

99 2AAB RLEYKPIKK-KVHVTK-a5-b1 sp|P11498|PYC sp|P11498|PYC 35 1159 1124

100 2AAB VIDIKVVAGAK-RLEYKPIKK-a5-b5 sp|P11498|PYC sp|P11498|PYC 1124 35 1089

101 2AAB KVMVANRGEIAIR-QKADEAYLIGR-a1-b2 sp|P11498|PYC sp|P11498|PYC 39 79 40

102 2AAB DVKGQIGAPMPGK-VVAGAKVAK-a3-b6 sp|P11498|PYC sp|P11498|PYC 1109 1130 21

103 2AAB HQKVVEIAPAAHLDPQLR-KMGDKVEAR-a3-b1 sp|P11498|PYC sp|P11498|PYC 273 148 125

104 2AAB AQKLLHYLGHVMVNGPTTPIPVK-SILVKDTQAMK-a3-b5 sp|P11498|PYC sp|P11498|PYC 499 1090 591

105 2AAB AYSEALAAFGNGALFVEKFIEKPR-HGKHYFIEVNSR-a18-b3 sp|P11498|PYC sp|P11498|PYC 237 319 82

106 2AAB GKTLHIK-FIEKPR-a2-b4 sp|P11498|PYC sp|P11498|PYC 1056 241 815

107 2AAB RLEYKPIKK-GKTLHIK-a8-b2 sp|P11498|PYC sp|P11498|PYC 38 1056 1018

108 2AAB VAKENNVDAVHPGYGFLSER-VIAHGKDHPTAATK-a3-b6 sp|P11498|PYC sp|P11498|PYC 107 434 327

109 2AAB KVMVANRGEIAIR-KMGDKVEAR-a1-b1 sp|P11498|PYC sp|P11498|PYC 39 148 109

110 2AAB VVAGAKVAK-KVHVTK-a6-b1 sp|P11498|PYC sp|P11498|PYC 1130 1159 29

111 2AAB FKEVKK-KVHVTK-a2-b1 sp|P11498|PYC sp|P11498|PYC 888 1159 271

70  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

112 2AAB VIAHGKDHPTAATK-RLEYKPIKK-a6-b8 sp|P11498|PYC sp|P11498|PYC 434 38 396

113 2AAB VAKENNVDAVHPGYGFLSER-GKTLHIK-a3-b2 sp|P11498|PYC sp|P11498|PYC 107 1056 949

114 2AAB KVMVANRGEIAIR-GKTLHIK-a1-b2 sp|P11498|PYC sp|P11498|PYC 39 1056 1017

115 2AAB TLHIKALAVSDLNR-VIAHGKDHPTAATK-a5-b6 sp|P11498|PYC sp|P11498|PYC 1061 434 627

116 2AAB VVAGAKVAK-ALKDVK-a6-b3 sp|P11498|PYC sp|P11498|PYC 1130 1106 24

117 2AAB QKADEAYLIGR-RLEYKPIKK-a2-b8 sp|P11498|PYC sp|P11498|PYC 79 38 41

118 2AAB SILVKDTQAMKEMHFHPK-VIAHGKDHPTAATK-a11-b6 sp|P11498|PYC sp|P11498|PYC 1096 434 662

119 2AAB VAKENNVDAVHPGYGFLSER-KVMVANR-a3-b1 sp|P11498|PYC sp|P11498|PYC 107 39 68

120 2AAB LAKQVGYENAGTVEFLVDRHGK-KMGDKVEAR-a3-b1 sp|P11498|PYC sp|P11498|PYC 300 148 152

121 SGOL1 SILVKDTQAMK-ALKDVK-a5-b3 sp|P11498|PYC sp|P11498|PYC 1090 1106 16

122 SGOL1 KMGDKVEAR-RLEYKPIKK-a1-b8 sp|P11498|PYC sp|P11498|PYC 148 38 110

123 SGOL1 HQKVVEIAPAAHLDPQLR-FIEKPR-a3-b4 sp|P11498|PYC sp|P11498|PYC 273 241 32

124 SGOL1 VAKENNVDAVHPGYGFLSER-RLEYKPIKK-a3-b5 sp|P11498|PYC sp|P11498|PYC 107 35 72

125 SGOL1 VAKENNVDAVHPGYGFLSER-KVHVTK-a3-b1 sp|P11498|PYC sp|P11498|PYC 107 1159 1052

126 SGOL1 QKADEAYLIGR-GKTLHIK-a2-b2 sp|P11498|PYC sp|P11498|PYC 79 1056 977

127 SGOL1 ALKDVK-KVHVTK-a3-b1 sp|P11498|PYC sp|P11498|PYC 1106 1159 53

128 SGOL1 VIAHGKDHPTAATK-RLEYKPIKK-a6-b5 sp|P11498|PYC sp|P11498|PYC 434 35 399

129 SGOL1 RLEYKPIKK-GKTLHIK-a5-b2 sp|P11498|PYC sp|P11498|PYC 35 1056 1021

130 SGOL1 KMGDKVEAR-RLEYKPIKK-a5-b8 sp|P11498|PYC sp|P11498|PYC 152 38 114

131 SGOL1 AQKLLHYLGHVMVNGPTTPIPVK-GKTLHIK-a3-b2 sp|P11498|PYC sp|P11498|PYC 499 1056 557

132 SGOL1 HQKVVEIAPAAHLDPQLR-MGDKVEAR-a3-b4 sp|P11498|PYC sp|P11498|PYC 273 152 121

133 SGOL1 VAKENNVDAVHPGYGFLSER-VIAHGKDHPTAATKMSR-a3-b14 sp|P11498|PYC sp|P11498|PYC 107 442 335

134 SGOL1 HGKHYFIEVNSR-GKTLHIK-a3-b2 sp|P11498|PYC sp|P11498|PYC 319 1056 737

135 SGOL1 VLKDLPR-KVHVTK-a3-b1 sp|P11498|PYC sp|P11498|PYC 969 1159 190

136 SGOL1 SILVKDTQAMKEMHFHPK-VIAHGKDHPTAATK-a5-b6 sp|P11498|PYC sp|P11498|PYC 1090 434 656

137 SGOL1 VAKENNVDAVHPGYGFLSER-QKADEAYLIGR-a3-b2 sp|P11498|PYC sp|P11498|PYC 107 79 28

138 IGBP1 VIAHGKDHPTAATK-KVHVTK-a6-b1 sp|P11498|PYC sp|P11498|PYC 434 1159 725

139 IGBP1 SILVKDTQAMK-KVHVTK-a5-b1 sp|P11498|PYC sp|P11498|PYC 1090 1159 69

140 IGBP1 VIAHGKDHPTAATK-GKTLHIK-a6-b2 sp|P11498|PYC sp|P11498|PYC 434 1056 622

141 IGBP1 VIAHGKDHPTAATKMSR-GKTLHIK-a14-b2 sp|P11498|PYC sp|P11498|PYC 442 1056 614

142 IGBP1 KMGDKVEAR-GKTLHIK-a5-b2 sp|P11498|PYC sp|P11498|PYC 152 1056 904

143 IGBP1 VIAHGKDHPTAATKMSR-RLEYKPIKK-a14-b5 sp|P11498|PYC sp|P11498|PYC 442 35 407

144 IGBP1 KMGDKVEAR-GKTLHIK-a1-b2 sp|P11498|PYC sp|P11498|PYC 148 1056 908

145 IGBP1 EMHFHPKALK-KVHVTK-a7-b1 sp|P11498|PYC sp|P11498|PYC 1103 1159 56

146 IGBP1 VIAHGKDHPTAATKMSR-RLEYKPIKK-a14-b8 sp|P11498|PYC sp|P11498|PYC 442 38 404

147 IGBP1 VIAHGKDHPTAATK-QKADEAYLIGR-a6-b2 sp|P11498|PYC sp|P11498|PYC 434 79 355

148 IGBP1 KMGDKVEAR-KVHVTK-a1-b1 sp|P11498|PYC sp|P11498|PYC 148 1159 1011

149 IGBP1 KMGDKVEAR-RLEYKPIKK-a5-b5 sp|P11498|PYC sp|P11498|PYC 152 35 117

150 IGBP1 TKYSLQYYMGLAEELVR-VLKDLPR-a2-b3 sp|P11498|PYC sp|P11498|PYC 717 969 252

151 IGBP1 KMGDKVEAR-KVHVTK-a5-b1 sp|P11498|PYC sp|P11498|PYC 152 1159 1007

152 IGBP1 AFHNEAQVNPERKNLK-DNKQAGVFEPTIVK-a13-b3 sp|P17987|TCPA sp|P17987|TCPA 481 499 18

153 IGBP1 SLKFATEAAITILR-LACKEAVR-a3-b4 sp|P17987|TCPA sp|P17987|TCPA 515 126 389

154 IGBP1 SLLVIPNTLAVNAAQDSTDLVAKLR-WIGLDLSNGKPR-a23-b10 sp|P17987|TCPA sp|P17987|TCPA 466 494 28

155 IGBP1 IVNAKIACLDFSLQK-ESDITKERIQK-a5-b6 sp|P17987|TCPA sp|P17987|TCPA 233 272 39

156 2ABG DCLINAAKTSMSSK-WIGLDLSNGKPR-a8-b10 sp|P17987|TCPA sp|P17987|TCPA 153 494 341

157 2ABG IVNAKIACLDFSLQK-NTKAR-a5-b3 sp|P17987|TCPA sp|P17987|TCPA 233 368 135

158 PP2AB RAAASKLGEFAK-QAAEDKSWR-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 188 255 67

159 2A5E FGKEWAHATIIPK-KLVEK-a3-b1 sp|P30153|2AAA sp|P30153|2AAA 475 468 7

160 2A5E VSSAVKAELR-AAASHKVK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 163 305 142

161 2A5E AISHEHSPSDLEAHFVPLVKR-LNSIKK-a20-b5 sp|P30153|2AAA sp|P30153|2AAA 133 33 100

162 2A5E EAATSNLKK-LVEKFGK-a8-b4 sp|P30153|2AAA sp|P30153|2AAA 467 472 5

163 2A5E RAAASKLGEFAK-AAASHKVK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 188 305 117

164 2A5E AISHEHSPSDLEAHFVPLVKR-AAASKLGEFAK-a20-b5 sp|P30153|2AAA sp|P30153|2AAA 133 188 55

165 2A5E RAAASKLGEFAK-LNSIKK-a6-b5 sp|P30153|2AAA sp|P30153|2AAA 188 33 155

166 SGOL1 DKAVESLR-LNSIKK-a2-b5 sp|P30153|2AAA sp|P30153|2AAA 107 33 74

167 2A5G AISHEHSPSDLEAHFVPLVKR-VSSAVKAELR-a20-b6 sp|P30153|2AAA sp|P30153|2AAA 133 163 30

168 2A5G ENVIMSQILPCIKELVSDANQHVK-TDLVPAFQNLMKDCEAEVR-a13-b12 sp|P30153|2AAA sp|P30153|2AAA 331 292 39

169 2A5G MTTLFCINVLSEVCGQDITTKHMLPTVLR-FGKEWAHATIIPK-a21-b3 sp|P30153|2AAA sp|P30153|2AAA 519 475 44

170 2A5G AISHEHSPSDLEAHFVPLVKR-LGEFAKVLELDNVK-a20-b6 sp|P30153|2AAA sp|P30153|2AAA 133 194 61

171 PP2AA FTELQKAVGPEITK-LGEFAKVLELDNVK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 272 194 78

172 PP2AA AISHEHSPSDLEAHFVPLVKR-DKAVESLR-a20-b2 sp|P30153|2AAA sp|P30153|2AAA 133 107 26

173 PP2AA SLQKIGPILDNSTLQSEVKPILEK-EAATSNLKK-a4-b8 sp|P30153|2AAA sp|P30153|2AAA 546 467 79

174 PP2AA FGKEWAHATIIPK-EAATSNLKK-a3-b8 sp|P30153|2AAA sp|P30153|2AAA 475 467 8

175 PP2AA ENVIMSQILPCIKELVSDANQHVK-DNTIEHLLPLFLAQLKDECPEVR-a13-b16 sp|P30153|2AAA sp|P30153|2AAA 331 374 43

176 PP2AB FTELQKAVGPEITK-VKEFCENLSADCR-a6-b2 sp|P30153|2AAA sp|P30153|2AAA 272 307 35

177 PP2AB AISHEHSPSDLEAHFVPLVKR-QAAEDKSWR-a20-b6 sp|P30153|2AAA sp|P30153|2AAA 133 255 122

178 PP2AB VSSAVKAELR-DKAVESLR-a6-b2 sp|P30153|2AAA sp|P30153|2AAA 163 107 56

179 PP2AB LGEFAKVLELDNVK-YMVADKFTELQK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 194 266 72

180 PP2AB VSSAVKAELR-QAAEDKSWR-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 163 255 92

181 2A5G AAASKLGEFAK-VSSAVKAELR-a5-b6 sp|P30153|2AAA sp|P30153|2AAA 188 163 25

182 2A5G YMVADKFTELQK-AAASHKVK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 266 305 39

183 2A5G AISHEHSPSDLEAHFVPLVKR-AAASHKVK-a20-b6 sp|P30153|2AAA sp|P30153|2AAA 133 305 172

184 2A5G RAAASKLGEFAK-DKAVESLR-a6-b2 sp|P30153|2AAA sp|P30153|2AAA 188 107 81

185 2A5G QAAEDKSWR-AAASHKVK-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 255 305 50

186 2A5G EWAHATIIPKVLAMSGDPNYLHR-QLSQSLLPAIVELAEDAKWR-a10-b18 sp|P30153|2AAA sp|P30153|2AAA 485 416 69

187 SGOL1 YMVADKFTELQK-QAAEDKSWR-a6-b6 sp|P30153|2AAA sp|P30153|2AAA 266 255 11

188 PP2AB RAAASKLGEFAK-QAAEDKSWR-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 200 267 67

189 2A5E ASNAVKAEIR-AAAAHKVK-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 175 317 142

71  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

190 2A5E IGPILDTNALQGEVKPVLQKLGQDEDMDVK-QMLPIVLKMAGDQVANVR-a20-b8 sp|P30154|2AAB sp|P30154|2AAB 578 539 39

191 2A5E RAAASKLGEFAK-LNSIKK-a6-b5 sp|P30154|2AAB sp|P30154|2AAB 200 45 155

192 2AAB RAAASKLGEFAK-ASNAVKAEIR-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 200 175 25

193 2AAB AAASKLGEFAK-AAAAHKVK-a5-b6 sp|P30154|2AAB sp|P30154|2AAB 200 317 117

194 2AAB IGPILDTNALQGEVKPVLQK-FNVAKSLQK-a15-b5 sp|P30154|2AAB sp|P30154|2AAB 573 554 19

195 2AAB LGEFAKVLELDSVK-ASNAVKAEIR-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 206 175 31

196 2AAB ASNAVKAEIR-QAAEDKSWR-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 175 267 92

197 2AAB YMVADRFSELQKAMGPK-AAASKLGEFAK-a12-b5 sp|P30154|2AAB sp|P30154|2AAB 284 200 84

198 2AAB QMLPIVLKMAGDQVANVR-FNVAKSLQK-a8-b5 sp|P30154|2AAB sp|P30154|2AAB 539 554 15

199 2AAB AAAAHKVK-DKAVESLR-a6-b2 sp|P30154|2AAB sp|P30154|2AAB 317 119 198

200 2AAB AAASKLGEFAK-LNSIKK-a5-b5 sp|P30154|2AAB sp|P30154|2AAB 200 45 155

201 2AAB KLSTIALALGVER-AAASKLGEFAK-a1-b5 sp|P30154|2AAB sp|P30154|2AAB 46 200 154

202 2AAB VLELDSVKSEIVPLFTSLASDEQDSVR-ASNAVKAEIR-a8-b6 sp|P30154|2AAB sp|P30154|2AAB 214 175 39

203 2AAB QISQEHTPVALEAYFVPLVKR-AAASKLGEFAK-a20-b5 sp|P30154|2AAB sp|P30154|2AAB 145 200 55

204 2AAB FSELQKAMGPK-QAAEDKSWR-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 284 267 17

205 SGOL1 DKAVESLR-LNSIKK-a2-b5 sp|P30154|2AAB sp|P30154|2AAB 119 45 74

206 2A5G QISQEHTPVALEAYFVPLVKR-ASNAVKAEIR-a20-b6 sp|P30154|2AAB sp|P30154|2AAB 145 175 30

207 PP2AB LGEFAKVLELDSVK-FSELQKAMGPK-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 206 284 78

208 PP2AB ASNAVKAEIR-DKAVESLR-a6-b2 sp|P30154|2AAB sp|P30154|2AAB 175 119 56

209 PP2AB QISQEHTPVALEAYFVPLVKR-DKAVESLR-a20-b2 sp|P30154|2AAB sp|P30154|2AAB 145 119 26

210 2A5G RAAASKLGEFAK-DKAVESLR-a6-b2 sp|P30154|2AAB sp|P30154|2AAB 200 119 81

211 2A5G QAAEDKSWR-AAAAHKVK-a6-b6 sp|P30154|2AAB sp|P30154|2AAB 267 317 50

212 IGBP1 KFIEDR-LVKAER-a1-b3 sp|P40227|TCPZ sp|P40227|TCPZ 265 261 4

213 IGBP1 HKSETDTSLIR-SVTLLIKGPNK-a2-b7 sp|P40227|TCPZ sp|P40227|TCPZ 199 377 178

214 IGBP1 FIEDRVKK-KIIELK-a7-b1 sp|P40227|TCPZ sp|P40227|TCPZ 272 273 1

215 PP4C KFIEDR-KIIELK-a1-b1 sp|P40227|TCPZ sp|P40227|TCPZ 265 273 8

216 PP4C TLNPKAEVAR-TNLGPKGTMK-a5-b6 sp|P40227|TCPZ sp|P40227|TCPZ 10 41 31

217 PP4C KVCGDSDK-KIIELKR-a1-b1 sp|P40227|TCPZ sp|P40227|TCPZ 280 273 7

218 PP4C KFIEDRVK-LVKAER-a1-b3 sp|P40227|TCPZ sp|P40227|TCPZ 265 261 4

219 PP4C SAEEREKLVK-KFIEDR-a7-b1 sp|P40227|TCPZ sp|P40227|TCPZ 258 265 7

220 PP4C GLVLDHGARHPDMKK-KIIELKR-a14-b6 sp|P40227|TCPZ sp|P40227|TCPZ 222 278 56

221 PP4C EKALQFLEEVK-HKPSVKGR-a2-b6 sp|P40227|TCPZ sp|P40227|TCPZ 129 430 301

222 PP4C GPNKHTLTQIK-HKSETDTSLIR-a4-b2 sp|P40227|TCPZ sp|P40227|TCPZ 381 199 182

223 PP4C GIDPFSLDALSKEGIVALRR-GLVLDHGARHPDMKK-a12-b14 sp|P40227|TCPZ sp|P40227|TCPZ 307 222 85

224 PP4C GLVLDHGARHPDMKK-FTFIEKCNNPR-a14-b6 sp|P40227|TCPZ sp|P40227|TCPZ 222 365 143

225 2ABG GLVLDHGARHPDMKK-HKSETDTSLIR-a14-b2 sp|P40227|TCPZ sp|P40227|TCPZ 222 199 23

226 2ABG MLVSGAGDIKLTK-HTLTQIKDAVR-a10-b7 sp|P40227|TCPZ sp|P40227|TCPZ 55 388 333

227 2ABG KVCGDSDK-IIELKRK-a1-b5 sp|P40227|TCPZ sp|P40227|TCPZ 280 278 2

228 2ABG KQLLHSCTVIATNILLVDEIMR-IITEGFEAAKEK-a1-b10 sp|P40227|TCPZ sp|P40227|TCPZ 502 127 375

229 IGBP1 TLNPKAEVAR-AGMSSLKG-a5-b7 sp|P40227|TCPZ sp|P40227|TCPZ 10 530 520

230 IGBP1 TKHKLDVTSVEDYK-ALQKYEK-a2-b4 sp|P48643|TCPE sp|P48643|TCPE 263 279 16

231 IGBP1 ISDSVLVDIKDTEPLIQTAK-LIKGVIVDK-a10-b3 sp|P48643|TCPE sp|P48643|TCPE 160 226 66

232 IGBP1 IAILTCPFEPPKPKTK-HKLDVTSVEDYK-a12-b2 sp|P48643|TCPE sp|P48643|TCPE 259 265 6

233 IGBP1 IAILTCPFEPPKPK-TKHKLDVTSVEDYK-a12-b2 sp|P48643|TCPE sp|P48643|TCPE 259 263 4

234 PP4C MLVIEQCKNSR-LIKGVIVDK-a8-b3 sp|P48643|TCPE sp|P48643|TCPE 378 226 152

235 PP4C HKLDVTSVEDYK-ALQKYEK-a2-b4 sp|P48643|TCPE sp|P48643|TCPE 265 279 14

236 PP4C KVEDAKIAILTCPFEPPKPK-MLVIEQCKNSR-a6-b8 sp|P48643|TCPE sp|P48643|TCPE 247 378 131

237 PP4C HKLDVTSVEDYKALQK-YEKEKFEEMIQQIK-a12-b3 sp|P48643|TCPE sp|P48643|TCPE 275 282 7

238 PP4C LGFAGLVQEISFGTTKDK-VGGRLEDTKLIK-a16-b9 sp|P48643|TCPE sp|P48643|TCPE 368 223 145

239 2ABG LEDTKLIK-VEGKVGGR-a5-b4 sp|P48643|TCPE sp|P48643|TCPE 223 214 9

240 2ABG MIIEEAKR-VEGKVGGR-a7-b4 sp|P48643|TCPE sp|P48643|TCPE 399 214 185

241 2ABG LEDTKLIK-KVEDAK-a5-b1 sp|P48643|TCPE sp|P48643|TCPE 223 242 19

242 2ABG GGNKMIIEEAKR-VEGKVGGR-a4-b4 sp|P48643|TCPE sp|P48643|TCPE 392 214 178

243 2ABG LIKGVIVDK-KVEDAK-a3-b1 sp|P48643|TCPE sp|P48643|TCPE 226 242 16

244 2ABG DKMLVIEQCK-KVEDAK-a2-b1 sp|P48643|TCPE sp|P48643|TCPE 370 242 128

245 IGBP1 DVDFELIKVEGK-MIIEEAKR-a8-b7 sp|P48643|TCPE sp|P48643|TCPE 210 399 189

246 2ABG EIQVQHPAAKSMIEISR-KKGDDQSR-a10-b1 sp|P49368|TCPG sp|P49368|TCPG 78 528 450

247 IGBP1 GASKEILSEVER-GVMINKDVTHPR-a4-b6 sp|P49368|TCPG sp|P49368|TCPG 381 222 159

248 IGBP1 IVSRPEELREDDVGTGAGLLEIKK-YIKNPR-a23-b3 sp|P49368|TCPG sp|P49368|TCPG 353 234 119

249 IGBP1 LQTYKTAVETAVLLLR-ALDDMISTLKK-a5-b10 sp|P49368|TCPG sp|P49368|TCPG 507 138 369

250 PP4C IDDIVSGHKK-KGDDQSR-a9-b1 sp|P49368|TCPG sp|P49368|TCPG 527 529 2

251 PP4C VEKIPGGIIEDSCVLR-GASKEILSEVER-a3-b4 sp|P49368|TCPG sp|P49368|TCPG 203 381 178

252 PP4C IGDEYFTFITDCKDPKACTILLR-YIKNPR-a16-b3 sp|P49368|TCPG sp|P49368|TCPG 370 234 136

253 PP4C LQTYKTAVETAVLLLR-KALDDMISTLKK-a5-b1 sp|P49368|TCPG sp|P49368|TCPG 507 128 379

254 2ABG GVMINKDVTHPR-YIKNPR-a6-b3 sp|P49368|TCPG sp|P49368|TCPG 222 234 12

255 2ABG EIQVQHPAAKSMIEISR-IDDIVSGHKK-a10-b9 sp|P49368|TCPG sp|P49368|TCPG 78 527 449

256 2ABG KVQSGNINAAK-IDDIVSGHKK-a1-b9 sp|P49368|TCPG sp|P49368|TCPG 21 527 506

257 2ABG EIQVQHPAAKSMIEISR-KKGDDQSR-a10-b2 sp|P49368|TCPG sp|P49368|TCPG 78 529 451

258 2ABG GVMINKDVTHPR-KTDNNR-a6-b1 sp|P49368|TCPG sp|P49368|TCPG 222 317 95

259 2ABG IGDEYFTFITDCKDPK-YIKNPR-a13-b3 sp|P49368|TCPG sp|P49368|TCPG 367 234 133

260 2ABG WSSLACNIALDAVKMVQFEENGR-KEIDIK-a14-b1 sp|P49368|TCPG sp|P49368|TCPG 181 191 10

261 2ABG GASKEILSEVER-KTDNNR-a4-b1 sp|P49368|TCPG sp|P49368|TCPG 381 317 64

262 2ABG KVQSGNINAAK-KKGDDQSR-a1-b2 sp|P49368|TCPG sp|P49368|TCPG 21 529 508

263 2ABG KVQSGNINAAK-KKGDDQSR-a1-b1 sp|P49368|TCPG sp|P49368|TCPG 21 528 507

264 2ABG EIDIKK-KTDNNR-a5-b1 sp|P49368|TCPG sp|P49368|TCPG 196 317 121

265 2ABG IVSRPEELREDDVGTGAGLLEIKK-GASKEILSEVER-a23-b4 sp|P49368|TCPG sp|P49368|TCPG 353 381 28

266 2ABG KGESQTDIEITREEDFTR-KTDNNR-a1-b1 sp|P49368|TCPG sp|P49368|TCPG 249 317 68

267 2ABG TAEELMNFSKGEENLMDAQVK-VADMALHYANKYNIMLVR-a10-b11 sp|P50990|TCPQ sp|P50990|TCPQ 270 307 37

72  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

268 2ABG IAVYSCPFDGMITETKGTVLIK-TAEELMNFSKGEENLMDAQVK-a16-b10 sp|P50990|TCPQ sp|P50990|TCPQ 254 270 16

269 PP4C RLCKTVGATALPR-LNSKWDLR-a4-b4 sp|P50990|TCPQ sp|P50990|TCPQ 326 318 8

270 2ABG AVDDGVNTFKVLTR-LCKTVGATALPR-a10-b3 sp|P50990|TCPQ sp|P50990|TCPQ 400 326 74

271 2ABG HEKEDGAISTIVLR-LCKTVGATALPR-a3-b3 sp|P50990|TCPQ sp|P50990|TCPQ 367 326 41

272 2ABG MVINHLEKLFVTNDAATILR-LNSKWDLR-a8-b4 sp|P50990|TCPQ sp|P50990|TCPQ 62 318 256

273 2ABG RLVPGGGATEIELAKQITSYGETCPGLEQYAIK-KAHEILPNLVCCSAK-a15-b1 sp|P50990|TCPQ sp|P50990|TCPQ 421 138 283

274 PP4C AYILNLVKQIK-KTGCNVLLIQK-a8-b1 sp|P50991|TCPD sp|P50991|TCPD 288 292 4

275 PP4C LGGTIDDCELVEGLVLTQKVSNSGITR-GSNKLVIEEAER-a19-b4 sp|P50991|TCPD sp|P50991|TCPD 232 395 163

276 2ABG FSNISAAKAVADAIR-DKPAQIR-a8-b2 sp|P50991|TCPD sp|P50991|TCPD 42 29 13

277 2ABG LLQKGIHPTIISESFQK-GKGAYQDR-a4-b2 sp|P50991|TCPD sp|P50991|TCPD 126 21 105

278 2ABG GAYQDRDKPAQIR-GKGAYQDR-a8-b2 sp|P50991|TCPD sp|P50991|TCPD 29 21 8

279 2ABG FSNISAAKAVADAIR-GKGAYQDRDKPAQIR-a8-b2 sp|P50991|TCPD sp|P50991|TCPD 42 21 21

280 2ABG ALEKGIEILTDMSRPVELSDR-HAQGEKTAGINVR-a4-b6 sp|P50991|TCPD sp|P50991|TCPD 143 489 346

281 IGBP1 KLGGTIDDCELVEGLVLTQK-GSNKLVIEEAER-a1-b4 sp|P50991|TCPD sp|P50991|TCPD 213 395 182

282 IGBP1 LLQKGIHPTIISESFQK-GKGAYQDRDKPAQIR-a4-b10 sp|P50991|TCPD sp|P50991|TCPD 126 29 97

283 IGBP1 CELIKESEVK-ALCAKAR-a5-b5 sp|P60510|PP4C sp|P60510|PP4C 21 31 10

284 PP4C VDSPVTVCGDIHGQFYDLKELFR-KYGSVTVWR-a19-b1 sp|P60510|PP4C sp|P60510|PP4C 63 133 70

285 PP2AB EILTKESNVQEVR-TLCEKAK-a5-b5 sp|P62714|PP2AB sp|P62714|PP2AB 41 34 7

286 PP2AB WLPQKNAAQFLLSTNDK-LWKISER-a5-b3 sp|P63151|2ABA sp|P63151|2ABA 105 123 18

287 PP2AB DITLEASRENNKPR-KVCASGKR-a12-b7 sp|P63151|2ABA sp|P63151|2ABA 387 402 15

288 PP2AB DITLEASRENNKPR-MFDRNTKR-a12-b7 sp|P63151|2ABA sp|P63151|2ABA 387 374 13

289 PP2AB DKRPEGYNLKEEDGR-LWKISER-a10-b3 sp|P63151|2ABA sp|P63151|2ABA 137 123 14

290 PP2AB KDEISVDSLDFNKK-TVLKPRK-a1-b4 sp|P63151|2ABA sp|P63151|2ABA 405 393 12

291 PP2AB DITLEASRENNKPR-KVCASGKR-a12-b1 sp|P63151|2ABA sp|P63151|2ABA 387 396 9

292 PP2AA KKDEISVDSLDFNK-TVLKPR-a1-b4 sp|P63151|2ABA sp|P63151|2ABA 404 393 11

293 PP2AA KKDEISVDSLDFNK-TVLKPR-a2-b4 sp|P63151|2ABA sp|P63151|2ABA 405 393 12

294 PP2AA KVCASGKR-TVLKPR-a7-b4 sp|P63151|2ABA sp|P63151|2ABA 402 393 9

295 PP2AA KKDEISVDSLDFNK-KVCASGKR-a1-b7 sp|P63151|2ABA sp|P63151|2ABA 404 402 2

296 PP2AA KKDEISVDSLDFNK-VCASGKRK-a2-b6 sp|P63151|2ABA sp|P63151|2ABA 405 402 3

297 PP2AA DKRPEGYNLKEEDGR-LWKISER-a2-b3 sp|P63151|2ABA sp|P63151|2ABA 129 123 6

298 PP2AA KVCASGK-TVLKPR-a1-b4 sp|P63151|2ABA sp|P63151|2ABA 396 393 3

299 PP4C DITLEASRENNKPR-TVLKPR-a12-b4 sp|P63151|2ABA sp|P63151|2ABA 387 393 6

300 PP2AB MFDRNTKR-TVLKPR-a7-b4 sp|P63151|2ABA sp|P63151|2ABA 374 393 19

301 PP2AB VVIFQQEQENKIQSHSR-ENNKPR-a11-b4 sp|P63151|2ABA sp|P63151|2ABA 62 387 325

302 PP2AB VVIFQQEQENKIQSHSR-DKRPEGYNLKEEDGR-a11-b2 sp|P63151|2ABA sp|P63151|2ABA 62 129 67

303 CT2NL YNIEKDIAAHIK-KEFDK-a5-b1 sp|P63167|DYL1 sp|P63167|DYL1 36 44 8

304 2A5E QLSESQVKSLCEK-AKEILTK-a8-b2 sp|P67775|PP2AA sp|P67775|PP2AA 29 36 7

305 IGBP1 EILTKESNVQEVR-SLCEKAK-a5-b5 sp|P67775|PP2AA sp|P67775|PP2AA 41 34 7

306 2A5G VFTKELDQWIEQLNECK-SLCEKAK-a4-b5 sp|P67775|PP2AA sp|P67775|PP2AA 8 34 26

307 2A5G KYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIR-QLSESQVKSLCEK-a9-b8

sp|P67775|PP2AA sp|P67775|PP2AA 144 29 115

308 2AAB LKAERER-TIEKFEK-a2-b4 sp|P68104|EF1A1 sp|P68104|EF1A1 64 41 23

309 FA40B QTVAVGVIKAVDK-KAAGAGK-a9-b1 sp|P68104|EF1A1 sp|P68104|EF1A1 439 444 5

310 FA40B KLEDGPKFLK-EKIDRR-a7-b2 sp|P68104|EF1A1 sp|P68104|EF1A1 392 378 14

311 FA40B QTVAVGVIKAVDKK-AAGAGKVTK-a9-b6 sp|P68104|EF1A1 sp|P68104|EF1A1 439 450 11

312 2ABG KLEDGPK-EKIDRR-a1-b2 sp|P68104|EF1A1 sp|P68104|EF1A1 386 378 8

313 FR1OP SGKKLEDGPK-EKIDRR-a3-b2 sp|P68104|EF1A1 sp|P68104|EF1A1 385 378 7

314 2AAB QLFHPEQLITGKEDAANNYAR-GHYTIGKEIIDLVLDR-a12-b7 sp|P68363|TBA1B sp|P68363|TBA1B 96 112 16

315 2AAB DVNAAIATIKTKR-LDHKFDLMYAKR-a12-b11 sp|P68363|TBA1B sp|P68363|TBA1B 338 401 63

316 2AAB DVNAAIATIKTKR-LDHKFDLMYAKR-a10-b11 sp|P68363|TBA1B sp|P68363|TBA1B 336 401 65

317 2AAB DVNAAIATIKTKR-LSVDYGKK-a10-b7 sp|P68363|TBA1B sp|P68363|TBA1B 336 163 173

318 2AAB TIGGGDDSFNTFFSETGAGKHVPR-LSVDYGKK-a20-b7 sp|P68363|TBA1B sp|P68363|TBA1B 60 163 103

319 PP2AB KAAQQQEEQEEKEEEDDEQTLHR-KYGALPDQGIAK-a1-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 295 276 19

320 PP2AB LSAMKSAVESGQADDERVR-YKQKK-a5-b4 sp|P78318|IGBP1 sp|P78318|IGBP1 176 165 11

321 PP2AB KAAQQQEEQEEKEEEDDEQTLHR-QVNPSKR-a12-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 306 97 209

322 PP2AB AREWDDWKDTHPR-QVNPSKR-a8-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 325 97 228

323 IGBP1 AREWDDWKDTHPR-QERPPVKPFILTR-a8-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 325 241 84

324 IGBP1 QERPPVKPFILTR-VFKGLDLLEK-a7-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 241 44 197

325 IGBP1 YGALPDQGIAKAAPEEFRK-YKQKK-a11-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 287 163 124

326 IGBP1 YGALPDQGIAKAAPEEFRK-AREWDDWKDTHPR-a11-b8 sp|P78318|IGBP1 sp|P78318|IGBP1 287 325 38

327 IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-KELEHR-a1-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 295 166 129

328 IGBP1 AREWDDWKDTHPR-KYGALPDQGIAK-a8-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 325 276 49

329 IGBP1 AREWDDWKDTHPR-KELEHR-a8-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 325 166 159

330 IGBP1 YGALPDQGIAKAAPEEFRK-KELEHR-a11-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 287 166 121

331 IGBP1 QERPPVKPFILTR-IVQEKVFK-a7-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 241 41 200

332 IGBP1 AREWDDWKDTHPR-YKQKK-a8-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 325 163 162

333 IGBP1 AREWDDWKDTHPR-QAKIQR-a8-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 325 158 167

334 IGBP1 AREWDDWKDTHPR-VFKGLDLLEK-a8-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 325 44 281

335 IGBP1 YGALPDQGIAKAAPEEFRK-QKKELEHR-a11-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 287 165 122

336 IGBP1 VFKGLDLLEK-QVNPSKR-a3-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 44 97 53

337 IGBP1 WIDISLEEIESIDQEIKILR-QERPPVKPFILTR-a17-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 216 241 25

338 IGBP1 AAQQQEEQEEKEEEDDEQTLHR-QERPPVKPFILTR-a11-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 306 241 65

339 IGBP1 LSAMKSAVESGQADDER-QAKIQR-a5-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 176 158 18

340 IGBP1 VFKGLDLLEK-QAKIQR-a3-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 44 158 114

341 IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-YGALPDQGIAKAAPEEFR-a1-b11 sp|P78318|IGBP1 sp|P78318|IGBP1 295 287 8

342 IGBP1 QKKELEHR-QAKIQR-a2-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 165 158 7

343 IGBP1 QERPPVKPFILTR-QKKELEHR-a7-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 241 166 75

344 IGBP1 EASTSNSSRQERPPVKPFILTR-KYGALPDQGIAK-a16-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 241 276 35

73  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

345 IGBP1 LSAMKSAVESGQADDERVR-QERPPVKPFILTR-a5-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 176 241 65

346 IGBP1 NMAQAKVFGAGYPSLPTMTVSDWYEQHR-AREWDDWKDTHPR-a6-b8 sp|P78318|IGBP1 sp|P78318|IGBP1 253 325 72

347 IGBP1 QERPPVKPFILTR-YKQKK-a7-b4 sp|P78318|IGBP1 sp|P78318|IGBP1 241 165 76

348 IGBP1 NMAQAKVFGAGYPSLPTMTVSDWYEQHRK-VFKGLDLLEK-a6-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 253 44 209

349 IGBP1 YLLVPAFQGALTMKQVNPSK-QERPPVKPFILTR-a14-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 91 241 150

350 IGBP1 VFKGLDLLEK-QKKELEHR-a3-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 44 166 122

351 IGBP1 AREWDDWKDTHPR-IVQEKVFK-a8-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 325 41 284

352 IGBP1 AAQQQEEQEEKEEEDDEQTLHR-KELEHR-a11-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 306 166 140

353 IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-IVQEKVFK-a1-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 295 41 254

354 IGBP1 KYGALPDQGIAK-IVQEKVFK-a1-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 276 41 235

355 IGBP1 NMAQAKVFGAGYPSLPTMTVSDWYEQHR-EASTSNSSRQERPPVKPFILTR-a6-b16

sp|P78318|IGBP1 sp|P78318|IGBP1 253 241 12

356 IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-VFKGLDLLEK-a1-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 295 44 251

357 IGBP1 YGALPDQGIAKAAPEEFRK-QVNPSKR-a11-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 287 97 190

358 IGBP1 NMAQAKVFGAGYPSLPTMTVSDWYEQHRK-KAAQQQEEQEEKEEEDDEQTLHR-a6-b1

sp|P78318|IGBP1 sp|P78318|IGBP1 253 295 42

359 IGBP1 NMAQAKVFGAGYPSLPTMTVSDWYEQHRK-YGALPDQGIAKAAPEEFRK-a6-b11 sp|P78318|IGBP1 sp|P78318|IGBP1 253 287 34

360 IGBP1 EASTSNSSRQERPPVKPFILTR-QVNPSKR-a16-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 241 97 144

361 PP2AA LSAMKSAVESGQADDERVR-KELEHR-a5-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 176 166 10

362 PP2AA KAAQQQEEQEEKEEEDDEQTLHR-KYGALPDQGIAK-a12-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 306 276 30

363 PP2AA NMAQAKVFGAGYPSLPTMTVSDWYEQHR-KYGALPDQGIAK-a6-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 253 276 23

364 PP2AA KAAQQQEEQEEKEEEDDEQTLHR-YKQKK-a1-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 295 163 132

365 PP4C AAQQQEEQEEKEEEDDEQTLHR-AREWDDWKDTHPR-a11-b8 sp|P78318|IGBP1 sp|P78318|IGBP1 306 325 19

366 PP4C YGALPDQGIAKAAPEEFRK-QERPPVKPFILTR-a11-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 287 241 46

367 PP4C KAAQQQEEQEEKEEEDDEQTLHR-YGALPDQGIAKAAPEEFR-a12-b11 sp|P78318|IGBP1 sp|P78318|IGBP1 306 287 19

368 PP2AB KELEHR-QAKIQR-a1-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 166 158 8

369 PP2AB KAAQQQEEQEEKEEEDDEQTLHR-AREWDDWKDTHPR-a1-b8 sp|P78318|IGBP1 sp|P78318|IGBP1 295 325 30

370 IGBP1 QERPPVKPFILTR-QAKIQR-a7-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 241 158 83

371 IGBP1 YGALPDQGIAKAAPEEFRK-QAKIQR-a11-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 287 158 129

372 IGBP1 QERPPVKPFILTR-YKQKK-a7-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 241 163 78

373 IGBP1 QAKIQR-YKQKK-a3-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 158 163 5

374 IGBP1 KYGALPDQGIAK-KELEHR-a1-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 276 166 110

375 IGBP1 LSAMKSAVESGQADDERVR-IVQEKVFK-a5-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 176 41 135

376 IGBP1 LSAMKSAVESGQADDERVR-KYGALPDQGIAK-a5-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 176 276 100

377 IGBP1 LSAMKSAVESGQADDERVR-YKQKK-a5-b2 sp|P78318|IGBP1 sp|P78318|IGBP1 176 163 13

378 IGBP1 KYGALPDQGIAK-QAKIQR-a1-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 276 158 118

379 IGBP1 NEDLEEIASTDLKYLLVPAFQGALTMK-LSAMKSAVESGQADDERVR-a13-b5 sp|P78318|IGBP1 sp|P78318|IGBP1 77 176 99

380 IGBP1 IVQEKVFK-QAKIQR-a5-b3 sp|P78318|IGBP1 sp|P78318|IGBP1 41 158 117

381 IGBP1 QVNPSKR-KELEHR-a6-b1 sp|P78318|IGBP1 sp|P78318|IGBP1 97 166 69

382 IGBP1 KAAQQQEEQEEKEEEDDEQTLHR-QERPPVKPFILTR-a1-b7 sp|P78318|IGBP1 sp|P78318|IGBP1 295 241 54

383 IGBP1 LSAMKSAVESGQADDERVR-QVNPSKR-a5-b6 sp|P78318|IGBP1 sp|P78318|IGBP1 176 97 79

384 2ABG ILKHGINCFINR-MKEKVER-a3-b2 sp|P78371|TCPB sp|P78371|TCPB 284 276 8

385 IGBP1 VRVDSTAKVAEIEHAEK-IKIFGSR-a8-b2 sp|P78371|TCPB sp|P78371|TCPB 263 250 13

386 IGBP1 VAEIEHAEKEK-MKEKVER-a9-b4 sp|P78371|TCPB sp|P78371|TCPB 272 278 6

387 IGBP1 EAVAMESYAKALR-EAESLIAKK-a10-b8 sp|P78371|TCPB sp|P78371|TCPB 441 119 322

388 IGBP1 VRVDSTAKVAEIEHAEK-MKEKVER-a8-b4 sp|P78371|TCPB sp|P78371|TCPB 263 278 15

389 IGBP1 VAEIEHAEKEK-IKIFGSR-a9-b2 sp|P78371|TCPB sp|P78371|TCPB 272 250 22

390 IGBP1 RIENAKILIANTGMDTDK-ILKHGINCFINR-a6-b3 sp|P78371|TCPB sp|P78371|TCPB 236 284 48

391 IGBP1 LTSFIGAIAIGDLVKSTLGPK-KIHPQTIIAGWR-a15-b1 sp|P78371|TCPB sp|P78371|TCPB 40 120 80

392 IGBP1 VAEIEHAEKEK-MKEKVER-a9-b2 sp|P78371|TCPB sp|P78371|TCPB 272 276 4

393 IGBP1 IKIFGSR-MKEKVER-a2-b4 sp|P78371|TCPB sp|P78371|TCPB 250 278 28

394 IGBP1 IKIFGSR-MKEKVER-a2-b2 sp|P78371|TCPB sp|P78371|TCPB 250 276 26

395 IGBP1 ILKHGINCFINR-MKEKVER-a3-b4 sp|P78371|TCPB sp|P78371|TCPB 284 278 6

396 IGBP1 VRVDSTAKVAEIEHAEK-MKEKVER-a8-b2 sp|P78371|TCPB sp|P78371|TCPB 263 276 13

397 PP4C LGSCKLIEEVMIGEDK-LKGSGNLEAIHIIK-a5-b2 sp|P78371|TCPB sp|P78371|TCPB 347 191 156

398 PP4C TPGKEAVAMESYAK-EAESLIAKK-a4-b8 sp|P78371|TCPB sp|P78371|TCPB 431 119 312

399 PP4C VRVDSTAKVAEIEHAEK-ILIANTGMDTDKIK-a8-b12 sp|P78371|TCPB sp|P78371|TCPB 263 248 15

400 PP4C SLHDALCVLAQTVKDSR-EATKAAR-a14-b4 sp|P78371|TCPB sp|P78371|TCPB 402 135 267

401 PP4C LLTHHKDHFTKLAVEAVLR-LKGSGNLEAIHIIKK-a6-b14 sp|P78371|TCPB sp|P78371|TCPB 176 203 27

402 2ABG SLHDALCVLAQTVKDSR-LKGSGNLEAIHIIK-a14-b2 sp|P78371|TCPB sp|P78371|TCPB 402 191 211

403 2ABG EALLSSAVDHGSDEVKFR-SLHDALCVLAQTVKDSR-a16-b14 sp|P78371|TCPB sp|P78371|TCPB 154 402 248

404 2ABG LKGSGNLEAIHIIKK-DHFTKLAVEAVLR-a14-b5 sp|P78371|TCPB sp|P78371|TCPB 203 181 22

405 2ABG LTSFIGAIAIGDLVKSTLGPK-EAVAMESYAKALR-a15-b10 sp|P78371|TCPB sp|P78371|TCPB 40 441 401

406 2ABG LKGSGNLEAIHIIK-DHFTKLAVEAVLR-a2-b5 sp|P78371|TCPB sp|P78371|TCPB 191 181 10

407 2ABG NIGVDNPAAKVLVDMSR-VDNIIKAAPR-a10-b6 sp|P78371|TCPB sp|P78371|TCPB 82 522 440

408 2ABG VDNIIKAAPR-KRVPDHHPC-a6-b1 sp|P78371|TCPB sp|P78371|TCPB 522 527 5

409 2ABG LTSFIGAIAIGDLVKSTLGPK-EAESLIAKK-a15-b8 sp|P78371|TCPB sp|P78371|TCPB 40 119 79

410 2ABG EALLSSAVDHGSDEVKFR-DHFTKLAVEAVLR-a16-b5 sp|P78371|TCPB sp|P78371|TCPB 154 181 27

411 2ABG RIENAKILIANTGMDTDK-LGSCKLIEEVMIGEDK-a6-b5 sp|P78371|TCPB sp|P78371|TCPB 236 347 111

412 2ABG EALLSSAVDHGSDEVKFR-LKGSGNLEAIHIIK-a16-b2 sp|P78371|TCPB sp|P78371|TCPB 154 191 37

413 IGBP1 LLTHHKDHFTK-STLGPKGMDK-a6-b6 sp|P78371|TCPB sp|P78371|TCPB 176 46 130

414 SGOL1 EFHLNESGDPSSKSTEIK-SSQTQNKASR-a13-b7 sp|Q01105|SET sp|Q01105|SET 167 189 22

415 SGOL1 SGYRIDFYFDENPYFENKVLSK-STEIKWK-a18-b5 sp|Q01105|SET sp|Q01105|SET 150 172 22

416 SGOL1 SSQTQNKASR-DLTKR-a7-b4 sp|Q01105|SET sp|Q01105|SET 189 181 8

417 SGOL1 SSQTQNKASR-SGKDLTKR-a7-b3 sp|Q01105|SET sp|Q01105|SET 189 177 12

418 PP4C ILAKLPIEPR-KLEAGIR-a4-b1 sp|Q08211|DHX9 sp|Q08211|DHX9 857 497 360

419 PP4C YGDGPRPPKMAR-FCEHKR-a9-b5 sp|Q08211|DHX9 sp|Q08211|DHX9 1163 943 220

420 PP2AB KVNNADDFPNLFR-LAKQSR-a1-b3 sp|Q13085|ACACA sp|Q13085|ACACA 323 353 30

74  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

421 PP2AB SSMSGLHLVKQGR-KKIDSQR-a10-b2 sp|Q13085|ACACA sp|Q13085|ACACA 86 93 7

422 PP2AB RLTFLVAQKDFR-KQVNYEVDRR-a9-b1 sp|Q13085|ACACA sp|Q13085|ACACA 1334 1338 4

423 PP2AB GSVLEPEGTVEIKFR-RKDLVK-a13-b2 sp|Q13085|ACACA sp|Q13085|ACACA 2127 2131 4

424 PP2AB EFPKFFTFRAR-DKFEEDRIYR-a4-b2 sp|Q13085|ACACA sp|Q13085|ACACA 1354 1363 9

425 PP2AB EFTQQNKATLVDHGIR-ARDKFEEDR-a7-b4 sp|Q13085|ACACA sp|Q13085|ACACA 1316 1363 47

426 PP2AB KAETLPEVEAELAQR-LELAEQKLQQTLR-a1-b7 sp|Q13136|LIPA1 sp|Q13136|LIPA1 384 377 7

427 PP2AB KAETLPEVEAELAQR-VAALSKAEER-a1-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 384 404 20

428 PP2AB ALDEKVRER-LFGKKEK-a5-b4 sp|Q13136|LIPA1 sp|Q13136|LIPA1 177 813 636

429 PP2AB LAALRDEPSKVQTLNEQDWER-RPQKGR-a10-b4 sp|Q13136|LIPA1 sp|Q13136|LIPA1 569 557 12

430 2A5G LELAEQKLQQTLR-VAALSKAEER-a7-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 377 404 27

431 2A5G KHELLEEARR-LGGQAEKNRK-a1-b7 sp|Q13136|LIPA1 sp|Q13136|LIPA1 861 854 7

432 2A5G SLFEHHKALDEK-MTVVKR-a7-b5 sp|Q13136|LIPA1 sp|Q13136|LIPA1 172 145 27

433 2A5G LIQEEKENTEQRAEEIESR-LQLHLKER-a6-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 650 467 183

434 2A5G ALKSLFEHHK-MTVVKR-a3-b5 sp|Q13136|LIPA1 sp|Q13136|LIPA1 165 145 20

435 2A5G LELAEQKLQQTLR-ITTLEKR-a7-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 377 327 50

436 PP2AA LQLHLKER-ITTLEKR-a6-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 467 327 140

437 PP2AA VIELQEIISKQSR-EQSQMKER-a10-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 261 270 9

438 PP2AA RLSDTVDKLLSESNER-ITTLEKR-a8-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 453 327 126

439 PP2AA KHELLEEARR-LGGQAEKNR-a1-b7 sp|Q13136|LIPA1 sp|Q13136|LIPA1 861 854 7

440 PP2AA KHELLEEARR-LNYDRKELER-a1-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 861 1032 171

441 PP2AB EAMAQKEDMEER-SEEMNTKLQR-a6-b7 sp|Q13136|LIPA1 sp|Q13136|LIPA1 315 303 12

442 PP2AB QMEAQLEEKNQELQR-VAALSKAEER-a9-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 426 404 22

443 PP2AB RFDEDDDKSFR-KREESQSEIK-a8-b1 sp|Q13136|LIPA1 sp|Q13136|LIPA1 1132 1037 95

444 2A5G MAALEDKNSLLR-LQLHLKER-a7-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 476 467 9

445 2A5G LSDTVDKLLSESNER-MNEEHNKR-a7-b7 sp|Q13136|LIPA1 sp|Q13136|LIPA1 453 445 8

446 2A5G EAMAQKEDMEER-LQLHLKER-a6-b6 sp|Q13136|LIPA1 sp|Q13136|LIPA1 315 467 152

447 2A5G QAQSPAGVSSEVEVLKALK-MTVVKR-a16-b5 sp|Q13136|LIPA1 sp|Q13136|LIPA1 162 145 17

448 2A5G VAALSKAEER-QTEDKNR-a6-b5 sp|Q13136|LIPA1 sp|Q13136|LIPA1 404 363 41

449 2A5G LGGQAEKNR-KLQKK-a7-b4 sp|Q13136|LIPA1 sp|Q13136|LIPA1 854 860 6

450 SGOL1 KALEAHCRADELASQDGR-KSELPQDPHTK-a1-b1 sp|Q13362|2A5G sp|Q13362|2A5G 507 496 11

451 SGOL1 MKEREEAWVK-LKEKLK-a2-b4 sp|Q13362|2A5G sp|Q13362|2A5G 424 420 4

452 SGOL1 LFDDCTQQFKAEK-LKEKLK-a10-b4 sp|Q13362|2A5G sp|Q13362|2A5G 413 420 7

453 SGOL1 LFDDCTQQFKAEKLK-NSKTHWNK-a10-b3 sp|Q13362|2A5G sp|Q13362|2A5G 413 379 34

454 SGOL1 KALEAHCR-KDRPLAR-a1-b1 sp|Q13362|2A5G sp|Q13362|2A5G 507 488 19

455 SGOL1 LFDDCTQQFKAEKLK-NSKTHWNK-a13-b3 sp|Q13362|2A5G sp|Q13362|2A5G 416 379 37

456 SGOL1 TVKDEAHQAQKDPK-KDRPLAR-a3-b1 sp|Q13362|2A5G sp|Q13362|2A5G 476 488 12

457 SGOL1 LFDDCTQQFKAEK-LKEKLK-a10-b2 sp|Q13362|2A5G sp|Q13362|2A5G 413 418 5

458 2A5G IYGKFLGLR-LFIQKLR-a4-b5 sp|Q13362|2A5G sp|Q13362|2A5G 192 45 147

459 2A5G KSELPQDPHTK-KDRPLAR-a1-b1 sp|Q13362|2A5G sp|Q13362|2A5G 496 488 8

460 2A5G MKEREEAWVK-KDRPLAR-a2-b1 sp|Q13362|2A5G sp|Q13362|2A5G 424 488 64

461 2A5G TIHGLIYNALKLFMEMNQK-NSKTHWNK-a11-b3 sp|Q13362|2A5G sp|Q13362|2A5G 395 379 16

462 2A5G EREEAWVKIENLAK-KDRPLAR-a8-b1 sp|Q13362|2A5G sp|Q13362|2A5G 432 488 56

463 2A5G LFIQKLR-WKEVKR-a5-b2 sp|Q13362|2A5G sp|Q13362|2A5G 45 66 21

464 2A5G YIDQKFVLQLLELFDSEDPRER-FLESPDFQPNIAKK-a5-b13 sp|Q13362|2A5G sp|Q13362|2A5G 162 156 6

465 2A5G IFLLKVLLPLHK-KQINNIFYR-a5-b1 sp|Q13362|2A5G sp|Q13362|2A5G 249 202 47

466 2A5G MKEREEAWVK-NSKTHWNK-a2-b3 sp|Q13362|2A5G sp|Q13362|2A5G 424 379 45

467 2A5G SELPQDPHTKK-KALEAHCR-a10-b1 sp|Q13362|2A5G sp|Q13362|2A5G 506 507 1

468 PP2AA TVKDEAHQAQKDPK-KDRPLAR-a11-b1 sp|Q13362|2A5G sp|Q13362|2A5G 484 488 4

469 PP2AA KTVKDEAHQAQK-KDRPLAR-a1-b1 sp|Q13362|2A5G sp|Q13362|2A5G 473 488 15

470 PP2AA FLESPDFQPNIAKK-IYGKFLGLR-a13-b4 sp|Q13362|2A5G sp|Q13362|2A5G 156 192 36

471 PP2AA KSELPQDPHTKK-KDRPLAR-a1-b1 sp|Q13362|2A5G sp|Q13362|2A5G 496 488 8

472 2A5G RKSELPQDPHTK-MKEREEAWVK-a2-b2 sp|Q13362|2A5G sp|Q13362|2A5G 496 424 72

473 2A5G IYGKFLGLR-KYIDQK-a4-b1 sp|Q13362|2A5G sp|Q13362|2A5G 192 157 35

474 2A5G DFLKTTLHR-IYGKFLGLR-a4-b4 sp|Q13362|2A5G sp|Q13362|2A5G 183 192 9

475 2A5G LFIQKLR-WKEVKR-a5-b5 sp|Q13362|2A5G sp|Q13362|2A5G 45 69 24

476 2A5G MKEREEAWVK-KALEAHCR-a2-b1 sp|Q13362|2A5G sp|Q13362|2A5G 424 507 83

477 2A5G MKEREEAWVK-AEKLK-a2-b3 sp|Q13362|2A5G sp|Q13362|2A5G 424 416 8

478 2A5G YIDQKFVLQLLELFDSEDPRER-KQINNIFYR-a5-b1 sp|Q13362|2A5G sp|Q13362|2A5G 162 202 40

479 2A5G DSTLTEPVVMALLKYWPK-QLAKCVSSPHFQVAER-a14-b4 sp|Q13362|2A5G sp|Q13362|2A5G 291 333 42

480 2A5G QLAKCVSSPHFQVAER-NSKTHWNK-a4-b3 sp|Q13362|2A5G sp|Q13362|2A5G 333 379 46

481 SGOL1 IYGKFLGLR-KQINNIFYR-a4-b1 sp|Q13362|2A5G sp|Q13362|2A5G 192 202 10

482 SGOL1 QCCVLFDFVSDPLSDLKWK-LFIQKLR-a17-b5 sp|Q13362|2A5G sp|Q13362|2A5G 64 45 19

483 SGOL1 FLESPDFQPNIAKK-KQINNIFYR-a13-b1 sp|Q13362|2A5G sp|Q13362|2A5G 156 202 46

484 FA40B IPTGQEYAAKIINTK-DHQKLER-a10-b4 sp|Q13557|KCC2D sp|Q13557|KCC2D 43 57 14

485 FA40B LLKHPNIVR-DHQKLER-a3-b4 sp|Q13557|KCC2D, sp|Q13555|KCC2G

sp|Q13557|KCC2D, sp|Q13555|KCC2G

69, 69 57, 57 12

486 FA40B LSARDHQKLER-IINTKK-a8-b5 sp|Q13557|KCC2D, sp|Q13555|KCC2G, sp|Q13554|KCC2B

sp|Q13557|KCC2D, sp|Q13555|KCC2G, sp|Q13554|KCC2B

57, 57, 57

48, 48, 48

9

487 PP2AB IKYSGGPQIVKK-KSELPQDVYTIK-a2-b1 sp|Q14738|2A5D sp|Q14738|2A5D 73 572 499

488 PP2AB KSELPQDVYTIK-ALEAHKR-a1-b6 sp|Q14738|2A5D sp|Q14738|2A5D 572 589 17

489 PP2AB LFDDCTQQYKAEKQK-NSKSHWNK-a13-b3 sp|Q14738|2A5D sp|Q14738|2A5D 492 455 37

490 SGOL1 LFDDCTQQYKAEKQK-NSKSHWNK-a10-b3 sp|Q14738|2A5D sp|Q14738|2A5D 489 455 34

491 PP2AA MKEREEMWQK-AEKQK-a2-b3 sp|Q14738|2A5D sp|Q14738|2A5D 500 492 8

492 PP2AA IKYSGGPQIVKK-DIKKEK-a2-b4 sp|Q14738|2A5D sp|Q14738|2A5D 73 564 491

493 PP2AA MKEREEMWQK-ALEAHKR-a2-b6 sp|Q14738|2A5D sp|Q14738|2A5D 500 589 89

494 PP2AA FLESPDFQPNIAKK-IYGKFLGLR-a13-b4 sp|Q14738|2A5D sp|Q14738|2A5D 232 268 36

495 PP2AA SHWNKTIHGLIYNALK-EKVLLRR-a5-b2 sp|Q14738|2A5D sp|Q14738|2A5D 460 566 106

496 PP2AA TIHGLIYNALKLFMEMNQK-NSKSHWNK-a11-b3 sp|Q14738|2A5D sp|Q14738|2A5D 471 455 16

75  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

497 PP2AA KSELPQDVYTIK-EKVLLR-a1-b2 sp|Q14738|2A5D sp|Q14738|2A5D 572 566 6

498 PP2AA ALEAHKR-EKVLLRR-a6-b2 sp|Q14738|2A5D sp|Q14738|2A5D 589 566 23

499 PP2AA IKYSGGPQIVKK-ALEAHKR-a2-b6 sp|Q14738|2A5D sp|Q14738|2A5D 73 589 516

500 PP2AA LRQCCVLFDFVSDPLSDLKFK-NRELQKLPALK-a19-b6 sp|Q14738|2A5D sp|Q14738|2A5D 140 102 38

501 PP2AA SHWNKTIHGLIYNALK-TVETEAVQMLKDIKK-a5-b11 sp|Q14738|2A5D sp|Q14738|2A5D 460 560 100

502 PP2AA KSELPQDVYTIKALEAHK-YSGGPQIVKK-a12-b9 sp|Q14738|2A5D sp|Q14738|2A5D 583 82 501

503 PP2AA KSELPQDVYTIK-DIKKEK-a1-b4 sp|Q14738|2A5D sp|Q14738|2A5D 572 564 8

504 PP2AA TVETEAVQMLKDIKK-EKVLLRR-a11-b2 sp|Q14738|2A5D sp|Q14738|2A5D 560 566 6

505 PP2AA TVETEAVQMLKDIKK-EKVLLR-a14-b2 sp|Q14738|2A5D sp|Q14738|2A5D 563 566 3

506 PP2AA EREEMWQKIEELAR-EKVLLR-a8-b2 sp|Q14738|2A5D sp|Q14738|2A5D 508 566 58

507 PP2AB QCCVLFDFVSDPLSDLKFK-FNLSKNR-a17-b5 sp|Q14738|2A5D sp|Q14738|2A5D 140 96 44

508 PP2AB APPPLPPVYSMETETPTAEDIQLLKR-LFDDCTQQYKAEK-a25-b10 sp|Q14738|2A5D sp|Q14738|2A5D 548 489 59

509 PP2AB ELQKLPALK-FNLSKNR-a4-b5 sp|Q14738|2A5D sp|Q14738|2A5D 102 96 6

510 PP2AB IKYSGGPQIVK-EKVLLR-a2-b2 sp|Q14738|2A5D sp|Q14738|2A5D 73 566 493

511 PP2AB DSPTQEREELFIQKLR-FNLSKNR-a14-b5 sp|Q14738|2A5D sp|Q14738|2A5D 121 96 25

512 PP2AB ESSLTEPVIVGLLKFWPK-QLAKCVSSPHFQVAER-a14-b4 sp|Q14738|2A5D sp|Q14738|2A5D 367 409 42

513 SGOL1 AEHKQFLMK-KIEEPLFK-a4-b1 sp|Q15172|2A5A sp|Q15172|2A5A 269 347 78

514 SGOL1 KALEKQNSAYNMHSILSNTSAE-LEELKLKK-a5-b5 sp|Q15172|2A5A sp|Q15172|2A5A 469 462 7

515 SGOL1 KALEKQNSAYNMHSILSNTSAE-LEELKLKK-a1-b7 sp|Q15172|2A5A sp|Q15172|2A5A 465 464 1

516 SGOL1 KLEELK-KALEK-a1-b1 sp|Q15172|2A5A sp|Q15172|2A5A 457 465 8

517 SGOL1 FLESPDFQPSIAKR-IYGKFLGLR-a13-b4 sp|Q15172|2A5A sp|Q15172|2A5A 181 217 36

518 SGOL1 FLESPDFQPSIAKR-KQINNIFLR-a13-b1 sp|Q15172|2A5A sp|Q15172|2A5A 181 227 46

519 SGOL1 KLEELKLK-KALEK-a6-b1 sp|Q15172|2A5A sp|Q15172|2A5A 462 465 3

520 PP2AA ILQEKLDQPVSAPPSPR-KASVTIQAR-a5-b1 sp|Q16204|CCDC6 sp|Q16204|CCDC7 234 96 138

521 PP4C MDKLEAEKR-FLKNEVER-a3-b3 sp|Q16204|CCDC6 sp|Q16204|CCDC7 223 266 43

522 PP2AB ILQEKLDQPVSAPPSPR-MDKLEAEKR-a5-b8 sp|Q16204|CCDC6 sp|Q16204|CCDC7 234 228 6

523 2A5E IYGKFLGLR-KQINNIFLR-a4-b1 sp|Q16537|2A5E sp|Q16537|2A5E 209 219 10

524 2A5E QFLVKVLIPLHTVR-KQINNIFLR-a5-b1 sp|Q16537|2A5E sp|Q16537|2A5E 266 219 47

525 2A5E QIAKCVSSPHFQVAER-GLMKFWPK-a4-b4 sp|Q16537|2A5E sp|Q16537|2A5E 350 308 42

526 2A5E QFLVKVLIPLHTVR-GLMKFWPK-a5-b4 sp|Q16537|2A5E sp|Q16537|2A5E 266 308 42

527 2A5E AFMEMNSTMFDELTATYKSDR-ISKEHWNPAIVALVYNVLK-a18-b3 sp|Q16537|2A5E sp|Q16537|2A5E 430 396 34

528 2A5E EKEREELWK-KLEDLELKR-a2-b8 sp|Q16537|2A5E sp|Q16537|2A5E 441 456 15

529 2A5E IQEPLFKQIAK-GLMKFWPK-a7-b4 sp|Q16537|2A5E sp|Q16537|2A5E 346 308 38

530 SGOL1 SQGKPIELTPLPLLK-DVPSSEQPELFLKK-a4-b13 sp|Q16537|2A5E sp|Q16537|2A5E 41 65 24

531 SGOL1 EKEREELWK-KLEDLELK-a2-b1 sp|Q16537|2A5E sp|Q16537|2A5E 441 449 8

532 SGOL1 LQQCCVIFDFMDTLSDLKMK-SQGKPIELTPLPLLK-a18-b4 sp|Q16537|2A5E sp|Q16537|2A5E 84 41 43

533 SGOL1 FLESQEFQPSIAKK-KQINNIFLR-a13-b1 sp|Q16537|2A5E sp|Q16537|2A5E 173 219 46

534 SGOL1 EDILESKSEQTK-LIQPGTFTKTK-a7-b9 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 276 267 9

535 SGOL1 MLVLALENEKSK-NLAEIGKR-a10-b7 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 72 35 37

536 SGOL1 NLAEIGKRR-MKEKR-a7-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 35 23 12

537 SGOL1 RNKNLAEIGK-NLAEIGKR-a3-b7 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 28 35 7

538 SGOL1 SFQDSLEDIKKR-NKNLAEIGK-a11-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 20 28 8

539 SGOL1 TKEDILESK-SEQTKSK-a2-b5 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 269 281 12

540 SGOL1 KSFQDSLEDIKK-RMKEK-a11-b3 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 19 23 4

541 SGOL1 TKEDILESKSEQTK-SKQRDTQER-a9-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 276 283 7

542 SGOL1 SFQDSLEDIKKR-NKNLAEIGK-a10-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 19 28 9

543 SGOL1 DQVNLSPKLIQPGTFTK-TKEDILESK-a8-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 258 269 11

544 SGOL1 SFQDSLEDIKKR-NLAEIGKR-a11-b7 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 20 35 15

545 SGOL1 DQVNLSPKLIQPGTFTK-TKEDILESKSEQTK-a8-b9 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 258 276 18

546 SGOL1 KSFQDSLEDIK-NLAEIGKR-a1-b7 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 9 35 26

547 SGOL1 CTASVNYKEPTLASK-ASPAVALPKRR-a8-b9 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 485 475 10

548 SGOL1 TKEDILESKSEQTK-SKQRDTQER-a2-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 269 283 14

549 SGOL1 EDILESKSEQTKSK-EEKRK-a12-b3 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 281 295 14

550 SGOL1 RNKNLAEIGK-ERCLKK-a3-b5 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 28 8 20

551 SGOL1 NLAEIGKRR-ENKSENKK-a7-b3 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 35 313 278

552 SGOL1 SFQDSLEDIKK-NLAEIGKR-a10-b7 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 19 35 16

553 SGOL1 NLAEIGKR-SSLKK-a7-b4 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 35 196 161

554 SGOL1 MLVLALENEKSK-VKEAQDIILQLR-a10-b2 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 72 76 4

555 SGOL1 YKENKSENK-KTVPQK-a5-b1 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 313 318 5

556 SGOL1 YKENKSENK-KTVPQKK-a2-b1 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 310 318 8

557 SGOL1 ENKSENKK-MSKYK-a3-b3 sp|Q5FBB7|SGOL1 sp|Q5FBB7|SGOL1 313 308 5

558 PP2AA LVSSEQALKELGLAEHQLR-LLHGTLIMKDSNFR-a9-b9 sp|Q5TA45|INT11 sp|Q5TA45|INT11 500 486 14

559 PP2AA VHLHDTRKEQETALR-VYSHLKSVLK-a8-b6 sp|Q5TA45|INT11 sp|Q5TA45|INT11 522 535 13

560 2A5G EAEPEKRPK-KVSQIR-a6-b1 sp|Q5THK1|PR14L sp|Q5THK1|PR14L 2005 2009 4

561 CT2NL KWTELDTNQHR-KCFEEDFR-a1-b1 sp|Q5VSL9|FA40A sp|Q5VSL9|FA40A 113 99 14

562 CT2NL KCFEEDFRIHVTDK-LKVAR-a1-b2 sp|Q5VSL9|FA40A sp|Q5VSL9|FA40A 99 143 44

563 CT2NL EKDIEMFLESSR-VQTKYLGR-a2-b4 sp|Q5VSL9|FA40A sp|Q5VSL9|FA40A 431 722 291

564 CT2NL SILGLPPLPEDSIKVIR-AAAGLLPGGKAR-a14-b10 sp|Q5VSL9|FA40A sp|Q5VSL9|FA40A 326 47 279

565 FR1OP VYKQAVFDLTK-GLDIESTSKR-a3-b9 sp|Q5VT06|CE350 sp|Q5VT06|CE351 2972 2968 4

566 FR1OP RVKNPNNLDEIK-LFSLKK-a3-b5 sp|Q5VT06|CE350 sp|Q5VT06|CE351 3013 3036 23

567 FR1OP LQQEKAEIKR-LQEANKAAR-a5-b6 sp|Q5VT06|CE350 sp|Q5VT06|CE351 1754 1765 11

568 FR1OP LQQEKAEIKR-LQEANKAAR-a9-b6 sp|Q5VT06|CE350 sp|Q5VT06|CE351 1758 1765 7

569 FR1OP ELGHDLHSISIPTKLLGCASK-VYKQAVFDLTK-a14-b3 sp|Q5VT06|CE350 sp|Q5VT06|CE351 2952 2972 20

570 PP2AB ASLKPR-ESSKPR-a4-b4 sp|Q66LE6|2ABD sp|Q66LE6|2ABD 399 393 6

571 2A5G LGSGYFSSNGKLEEVK-LEEVKTPK-a11-b5 sp|Q69YH5|CDCA2 sp|Q69YH5|CDCA2 622 627 5

572 PP4C KHREFLTK-TAKFK-a1-b3 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 235 245 10

573 PP4C QDNPKLDSMR-GLKLR-a5-b3 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 655 641 14

574 PP4C AESDGSLLLESKINPNTAYQK-LKGMSLLVR-a12-b2 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 55 36 19

76  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

575 PP4C VKVYTLNEDR-LKGMSLLVR-a2-b2 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 9 36 27

576 PP4C YIMKSFLFEPVVK-ERQDNPKLDSMR-a4-b7 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 576 655 79

577 PP4C EVLLKTNLSGR-LKESEEK-a5-b2 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 733 723 10

578 PP4C KHREFLTK-QKIHQTYR-a1-b2 sp|Q6IN85|P4R3A sp|Q6IN85|P4R3A 235 260 25

579 PP4C EILPLVKSLCQDVEYEVR-LTNKFDAHTIKR-a7-b11 sp|Q6NUP7|PP4R4 sp|Q6NUP7|PP4R4 218 210 8

580 PP2AA DGLCLSESETVNKER-ANSYKNPR-a13-b5 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 295 302 7

581 PP2AA AGFLHHVKK-LWKTPPREK-a8-b3 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 554 540 14

582 PP2AA SVSKTPDESTK-TKDQILTSR-a4-b2 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 750 759 9

583 PP2AA FKSQLPDLSGPHSYSPGR-QSWPSPAVKGR-a2-b9 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 883 879 4

584 PP2AA DKATTSGSNSISVR-KAQQETGER-a2-b1 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 626 611 15

585 PP2AA IAKMSLSPSSPR-KAQQETGER-a3-b1 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 800 611 189

586 PP2AA TPPREKAGFLHHVK-KSDPERGFER-a6-b1 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 546 555 9

587 PP2AA NSVAGSNPAKPGLGSPGR-KAQQETGER-a10-b1 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 909 611 298

588 PP2AB TQDLTAKLR-ANSYKNPR-a7-b5 sp|Q86XL3|ANKL2 sp|Q86XL3|ANKL2 312 302 10

589 PP2AA RPSAAAKPSGHPPPGDFIALGSK-AKPTTVR-a7-b2 sp|Q8N201|INT1 sp|Q8N201|INT1 17 5 12

590 2AAB QASLHVWKIVVSNTPR-HLDKSDPK-a8-b4 sp|Q92616|GCN1L sp|Q92616|GCN1L 1909 1332 577

591 FA40B ELQVKQQLDSCVTK-AKDSIDAGSK-a5-b2 sp|Q96C01|F136A sp|Q96C01|F136A 104 91 13

592 PP2AA LVDVACKHLTDTSHGVR-SVTKDAEGLAAR-a7-b4 sp|Q96HW7|INT4 sp|Q96HW7|INT4 157 186 29

593 2A5E RIGYPVMIKAVR-DMGIKSTSK-a9-b5 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 205 163 42

594 2AAB KSFNDDAMLIEK-GGGGKGMR-a1-b5 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 237 213 24

595 2AAB HQKIIEEAPAPGIK-GGGGKGMR-a3-b5 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 284 213 71

596 2AAB ESLCQAALGLILKEK-NITKVLIANR-a13-b4 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 518 51 467

597 2AAB NITKVLIANRGEIACR-QAALTKLR-a4-b6 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 51 450 399

598 SGOL1 IIEEAPAPGIKSEVR-KKLGEAAVR-a11-b1 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 295 300 5

599 SGOL1 HTPLVEFEEEESDKRESE-AGDKVK-a14-b4 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 721 667 54

600 SGOL1 HQKIIEEAPAPGIK-KLGEAAVR-a3-b1 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 284 301 17

601 SGOL1 IIEEAPAPGIKSEVR-GGGGKGMR-a11-b5 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 295 213 82

602 SGOL1 ESLCQAALGLILKEK-QAALTKLR-a13-b6 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 518 450 68

603 IGBP1 RIGYPVMIKAVR-GGGGKGMR-a9-b5 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 205 213 8

604 IGBP1 IIEEAPAPGIKSEVR-KKLGEAAVR-a11-b2 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 295 301 6

605 IGBP1 IAAGEKIPLSQEEITLQGHAFEAR-IIEEAPAPGIKSEVR-a6-b11 sp|Q96RQ3|MCCA sp|Q96RQ3|MCCA 367 295 72

606 2ABG YNFFTGCPKAK-VPEEDLKR-a9-b7 sp|Q99832|TCPH sp|Q99832|TCPH 366 320 46

607 IGBP1 KLLEKCAMTALSSK-KADKVEQR-a5-b1 sp|Q99832|TCPH sp|Q99832|TCPH 157 145 12

608 IGBP1 LLEKCAMTALSSK-LISQQKAFFAK-a4-b6 sp|Q99832|TCPH sp|Q99832|TCPH 157 172 15

609 IGBP1 VVLSKLPIGDVATQYFADRDMFCAGR-VPEEDLKR-a5-b7 sp|Q99832|TCPH sp|Q99832|TCPH 292 320 28

610 IGBP1 KLLEKCAMTALSSK-KADKVEQR-a5-b4 sp|Q99832|TCPH sp|Q99832|TCPH 157 148 9

611 IGBP1 KLLEKCAMTALSSK-KADKVEQR-a1-b4 sp|Q99832|TCPH sp|Q99832|TCPH 153 148 5

612 IGBP1 QQLLIGAYAKALEIIPR-QVKPYVEEGLHPQIIIR-a10-b3 sp|Q99832|TCPH sp|Q99832|TCPH 440 109 331

613 PP4C MVVDAVMMLDDLLQLKMIGIKK-VPEEDLKR-a16-b7 sp|Q99832|TCPH sp|Q99832|TCPH 193 320 127

614 2ABG IKEIAVTVK-KADKVEQR-a2-b1 sp|Q99832|TCPH sp|Q99832|TCPH 137 145 8

615 2ABG KYHNPKIALLNVELELK-YNFFTGCPKAK-a6-b9 sp|Q99832|TCPH sp|Q99832|TCPH 236 366 130

616 2ABG IKEIAVTVK-ADKVEQRK-a2-b3 sp|Q99832|TCPH sp|Q99832|TCPH 137 148 11

617 2ABG IHHSGAKVVLSK-KYHNPK-a7-b1 sp|Q99832|TCPH sp|Q99832|TCPH 287 231 56

618 2ABG KADKVEQR-KLLEK-a1-b1 sp|Q99832|TCPH sp|Q99832|TCPH 145 153 8

619 2ABG VVLSKLPIGDVATQYFADRDMFCAGR-GKATISNDGATILK-a5-b2 sp|Q99832|TCPH sp|Q99832|TCPH 292 55 237

620 IGBP1 INALTAASEAACLIVSVDETIKNPR-LLDVVHPAAKTLVDIAK-a22-b10 sp|Q99832|TCPH sp|Q99832|TCPH 521 77 444

621 2A5G ASKDQVLSEPETK-GKEPR-a3-b2 sp|Q9BWN1|PRR14 sp|Q9BWN1|PRR14 428 422 6

622 2A5E LGGGEKAR-GKLLPR-a6-b2 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 70 80 10

623 2A5E EGKQFSSADEAALKEPIIK-LGGGEKAR-a14-b6 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 506 70 436

624 2AAB KSGVSDHWALDDHHALHLTR-EYEAEGIAKDGAK-a1-b9 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 269 420 151

625 2AAB KSGVSDHWALDDHHALHLTR-KQGTIFLAGPPLVK-a1-b1 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 269 235 34

626 2AAB ISVMGGEQAANVLATITKDQR-QFSSADEAALKEPIIK-a18-b11 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 487 506 19

627 2AAB KLDVTIEPSEEPLFPADELYGIVGANLKR-QFSSADEAALKEPIIK-a28-b11 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 326 506 180

628 2AAB ISVMGGEQAANVLATITKDQR-EGKQFSSADEAALKEPIIK-a18-b3 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 487 495 8

629 2AAB QFSSADEAALKEPIIK-KFEEEGNPYYSSAR-a11-b1 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 506 512 6

630 SGOL1 AREGKQFSSADEAALK-LGGGEKAR-a5-b6 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 495 70 425

631 SGOL1 VSGVECMIIANDATVKGGAYYPVTVKK-LGGGEKAR-a16-b6 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 141 70 71

632 SGOL1 KQGTIFLAGPPLVK-GKLLPR-a1-b2 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 235 80 155

633 SGOL1 VSGVECMIIANDATVKGGAYYPVTVKK-KFEEEGNPYYSSAR-a16-b1 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 141 512 371

634 IGBP1 KSGVSDHWALDDHHALHLTR-GKLLPR-a1-b2 sp|Q9HCC0|MCCB sp|Q9HCC0|MCCB 269 80 189

635 CT2NL KNAALDVEPIHAFR-TWNPKFTLR-a1-b5 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 475 431 44

636 CT2NL KNAALDVEPIHAFR-LWNLQKAVTAK-a1-b6 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 475 469 6

637 CT2NL KHEEAIHAVACHPSKALIASAGADALAK-TWNPKFTLR-a15-b5 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 737 431 306

638 CT2NL ALIASAGADALAKVFV-KNAALDVEPIHAFR-a13-b1 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 750 475 275

639 CT2NL KHEEAIHAVACHPSKALIASAGADALAK-KTWNPKFTLR-a15-b1 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 737 426 311

640 CT2NL KHEEAIHAVACHPSKALIASAGADALAK-KTWNPKFTLR-a1-b6 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 723 431 292

641 CT2NL NAAGKDGKER-QIEEQIKR-a8-b7 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 254 245 9

642 CT2NL LWNLQKAVTAK-TWNPKFTLR-a6-b5 sp|Q9NRL3|STRN4 sp|Q9NRL3|STRN4 469 431 38

643 CT2NL MLEYALKQER-YHKLK-a7-b3 sp|Q9NRL3|STRN4, sp|O43815|STRN, sp|Q13033|STRN3

sp|Q9NRL3|STRN4, sp|O43815|STRN, sp|Q13033|STRN3

126, 110, 126

134, 118, 134

8

644 PP2AA AHINNSEKHQR-AVKDYEQEK-a8-b3 sp|Q9NVM9|M89BB sp|Q9NVM9|M89BB 549 589 40

645 PP2AB AHINNSEKHQR-LKGILER-a8-b2 sp|Q9NVM9|M89BB sp|Q9NVM9|M89BB 549 604 55

646 PP2AB AHINNSEKHQR-KHQEFAGR-a8-b1 sp|Q9NVM9|M89BB sp|Q9NVM9|M89BB 549 668 119

647 PP4C NKHPDEDAVEAEGHEVKR-FDKEGEVR-a17-b3 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 246 252 6

648 PP4C NKHPDEDAVEAEGHEVK-FDKEGEVR-a2-b3 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 231 252 21

649 PP4C GKKEVCPVLDQFLCHVAK-LEKVMDDFR-a3-b3 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 19 55 36

650 PP4C KEVCPVLDQFLCHVAK-DFEKRGK-a1-b4 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 19 15 4

77  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

651 PP4C GKKEVCPVLDQFLCHVAK-TGETMIQWSQFKGYFIFK-a3-b12 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 19 46 27

652 PP4C NKHPDEDAVEAEGHEVKR-DKDSR-a17-b2 sp|Q9NY27|PP4R2 sp|Q9NY27|PP4R2 246 287 41

653 CT2NL SRVSKLEEELAAER-AGELSLKLEKEK-a5-b7 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 216 206 10

654 CT2NL HAQDTAEGDDVTYMLEKERER-KVILDLEEERQR-a17-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 138 110 28

655 CT2NL SRVSKLEEELAAER-AGELSLKLEKEK-a5-b10 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 216 209 7

656 CT2NL IVKDLEASHQHSSPNEQLK-TLKEEMESLKK-a3-b10 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 275 271 4

657 CT2NL HKFQSQADQDQQASGLQSPPSR-DLSPTLIDNSAAKQLAR-a2-b13 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 465 498 33

658 CT2NL QPVCTNPLSILKVVMK-DFETLKEK-a12-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 84 65 19

659 CT2NL DLEASHQHSSPNEQLKKPVTVSK-KPVTVSK-a16-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 291 292 1

660 CT2NL AAEEGQKAGELSLK-LEKEK-a7-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 199 209 10

661 CT2NL IVKDLEASHQHSSPNEQLK-KPVTVSK-a3-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 275 292 17

662 CT2NL YGKYNISDPLMALQR-DFETLKEK-a3-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 47 65 18

663 CT2NL DLVIEALKAQHR-DFETLKEK-a8-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 33 65 32

664 CT2NL FTSQQGPIKPVSPNSSPFGTDYR-DLSPTLIDNSAAKQLAR-a9-b13 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 520 498 22

665 CT2NL AGELSLKLEKEK-AKLNREENR-a10-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 209 252 43

666 CT2NL VSKLEEELAAERK-LEKEKSR-a3-b5 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 216 211 5

667 CT2NL VSKLEEELAAER-AKLNREENR-a3-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 216 252 36

668 CT2NL FTSQQGPIKPVSPNSSPFGTDYR-VSSPLSPLSPGIKSPTIPR-a9-b13 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 520 567 47

669 CT2NL IVKDLEASHQHSSPNEQLK-TLKEEMESLKK-a3-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 275 264 11

670 CT2NL DLVIEALKAQHRDTFIEER-YGKYNISDPLMALQR-a8-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 33 47 14

671 CT2NL AKLNREENR-EENRTKTLK-a2-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 252 261 9

672 CT2NL AKLNREENR-KPVTVSK-a2-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 252 292 40

673 CT2NL IVKDLEASHQHSSPNEQLK-AKLNREENR-a3-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 275 252 23

674 CT2NL TLKEEMESLKK-AKLNREENR-a10-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 271 252 19

675 CT2NL QPVCTNPLSILKVVMK-EKNDGEK-a12-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 84 67 17

676 CT2NL HAQDTAEGDDVTYMLEKERER-YGKYNISDPLMALQR-a17-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 138 47 91

677 CT2NL DLEASHQHSSPNEQLKKPVTVSK-IVKDLEASHQHSSPNEQLK-a16-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 291 275 16

678 CT2NL KVILDLEEERQR-SQVKK-a1-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 110 155 45

679 CT2NL DLVIEALKAQHRDTFIEER-EKNDGEKQPVCTNPLSILK-a8-b7 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 33 72 39

680 CT2NL DLVIEALKAQHR-KVILDLEEERQR-a8-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 33 110 77

681 CT2NL VSSPLSPLSPGIKSPTIPR-DLSPTLIDNSAAKQLAR-a13-b13 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 567 498 69

682 CT2NL EKNDGEKQPVCTNPLSILK-YGKYNISDPLMALQR-a7-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 72 47 25

683 CT2NL DLEASHQHSSPNEQLKKPVTVSK-TLKEEMESLKK-a16-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 291 264 27

684 CT2NL LTQQLEFEKSQVK-KVILDLEEER-a9-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 151 110 41

685 CT2NL KLSSQLEEER-FEKEQK-a1-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 163 159 4

686 CT2NL HAQDTAEGDDVTYMLEKER-LTQQLEFEKSQVK-a17-b9 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 138 151 13

687 CT2NL YGKYNISDPLMALQR-KVILDLEEERQR-a3-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 47 110 63

688 CT2NL DLVIEALKAQHR-VVMKQCK-a8-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 33 88 55

689 CT2NL KRGLQTEAQVEK-VSKLEEELAAER-a1-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 226 216 10

690 CT2NL TLKEEMESLKK-AKLNREENR-a3-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 264 252 12

691 CT2NL TLKEEMESLKK-KPVTVSK-a10-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 271 292 21

692 CT2NL KRGLQTEAQVEK-AKLNREENR-a1-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 226 252 26

693 CT2NL NDGEKQPVCTNPLSILK-DFETLKEK-a5-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 72 65 7

694 CT2NL AGELSLKLEKEK-AKLNREENR-a7-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 206 252 46

695 CT2NL QLSSMLVLECKK-ATNKAAEEGQK-a11-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 187 192 5

696 CT2NL YGKYNISDPLMALQR-VVMKQCK-a3-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 47 88 41

697 CT2NL KLSSQLEEER-SQVKKFEK-a1-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 163 155 8

698 CT2NL KLSSQLEEER-FEKEQKK-a1-b6 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 163 162 1

699 CT2NL ATNKAAEEGQK-KLSSQLEEER-a4-b1 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 192 163 29

700 CT2NL KRGLQTEAQVEK-KFEKEQK-a1-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 226 159 67

701 CT2NL KPGLTPSPSATTPLTK-AKLNREENR-a1-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 586 252 334

702 CT2NL FTSQQGPIKPVSPNSSPFGTDYR-HKFQSQADQDQQASGLQSPPSR-a9-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 520 465 55

703 CT2NL KLSSQLEEERSR-SQVKKFEK-a1-b5 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 163 156 7

704 CT2NL YGKYNISDPLMALQR-QCKNMQER-a3-b3 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 47 91 44

705 CT2NL FTSQQGPIKPVSPNSSPFGTDYR-ATNKAAEEGQK-a9-b4 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 520 192 328

706 CT2NL GDTSHSPTPGKVSSPLSPLSPGIK-DLSPTLIDNSAAKQLAR-a11-b13 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 554 498 56

707 CT2NL GDTSHSPTPGKVSSPLSPLSPGIK-FTSQQGPIKPVSPNSSPFGTDYR-a11-b9 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 554 520 34

708 CT2NL FTSQQGPIKPVSPNSSPFGTDYR-AKLNREENR-a9-b2 sp|Q9P2B4|CT2NL sp|Q9P2B4|CT2NL 520 252 268

709 FA40B VRQKDIEHFLEMSR-VAFPKGLPWAPK-a4-b5 sp|Q9ULQ0|FA40B sp|Q9ULQ0|FA40B 427 416 11

710 FA40B VAFPKGLPWAPK-GKQAAPK-a5-b2 sp|Q9ULQ0|FA40B sp|Q9ULQ0|FA40B 416 25 391

711 FA40B QKDIEHFLEMSR-GLPWAPKVR-a2-b7 sp|Q9ULQ0|FA40B sp|Q9ULQ0|FA40B 427 423 4

712 CT2NL VAFPKGLPWAPK-TMSAIYQKVR-a5-b8 sp|Q9ULQ0|FA40B sp|Q9ULQ0|FA40B 416 738 322

713 2ABG MFDRNTKR-RVCVGGKR-a7-b7 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 370 398 28

714 2ABG SFFSEIISSVSDVKFSHSGR-AVLKPR-a14-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 288 389 101

715 2ABG SFFSEIISSVSDVKFSHSGR-HSKLFEEPEDPSNR-a14-b3 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 288 263 25

716 2ABG RVCVGGKR-AVLKPR-a7-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 398 389 9

717 2ABG DDISVDSLDFTKK-AVLKPR-a12-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 413 389 24

718 2ABG DKRPEGYNLK-DEEGKLK-a2-b5 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 125 138 13

719 2ABG DYLTVKVWDLNMEARPIETYQVHDYLR-AVLKPR-a6-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 305 389 84

720 2ABG SKLCSLYENDCIFDK-AVLKPR-a2-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 328 389 61

721 2ABG RVCVGGKR-ESSKPR-a7-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 398 383 15

722 2ABG MFDRNTKR-ESSKPR-a7-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 370 383 13

723 2ABG MFDRNTKR-AVLKPR-a7-b4 sp|Q9Y2T4|2ABG sp|Q9Y2T4|2ABG 370 389 19

724 CT2NL HTLDGAACLLNSNKYFPSR-VSIKESSVAK-a14-b4 sp|Q9Y3A3|MOBL3 sp|Q9Y3A3|MOBL3 140 149 9

725 CT2NL HTLDGAACLLNSNKYFPSR-ESSVAKLGSVCR-a14-b6 sp|Q9Y3A3|MOBL3 sp|Q9Y3A3|MOBL3 140 155 15

726 CT2NL ILEPPEGQDEGVWKYEHLR-VSIKESSVAK-a14-b4 sp|Q9Y3A3|MOBL3 sp|Q9Y3A3|MOBL3 70 149 79

727 PP2AB KEDDMETKK-KDHPYTWR-a8-b1 sp|Q9Y570|PPME1 sp|Q9Y570|PPME1 280 281 1

728 PP2AA IELAKTEK-GRPKTFK-a5-b4 sp|Q9Y570|PPME1 sp|Q9Y570|PPME1 293 203 90

78  

No. Bait Topology Protein1 Protein2 Pos1 Pos2 ∆AA

729 PP2AA KKEDDMETK-KDHPYTWR-a2-b1 sp|Q9Y570|PPME1 sp|Q9Y570|PPME1 273 281 8

730 PP2AA KKEDDMETK-KDHPYTWR-a1-b1 sp|Q9Y570|PPME1 sp|Q9Y570|PPME1 272 281 9

731 PP2AB VSMVGQVKQCEGITSPEGSK-IELAKTEK-a8-b5 sp|Q9Y570|PPME1 sp|Q9Y570|PPME1 236 293 57

79  

Table S5.2.

(No., cross-link identifier; N_Id, number of fragment ion spectra assigned to the cross-link in

entire dataset; N_Exp, number of experiments identifying the cross-link; m/z, precursor mass

to charge ratio; z, precursor charge; Error, mass deviation from the monoisotopic precursor

mass in ppm; Tic, relative contribution to total ion current; Id-Score, xQuest identification

score; X ions, minimum number of cross-link ions per peptide and cross-link; PDB, PDB

entry of protein structure for evaluation of cross-link distances; Euclidean, Euclidean cross-

link distance measured in PDB structure or comparative model in Å; SAS, solvent-accessible

surface (SAS) cross-link distance measured in PDB structure or comparative model in Å)

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

1 2 1 739.647 4 0.4 0.45 33.2 4

2 2 1 856.12 3 2.6 0.38 26.74 2

3 2 1 435.76 4 1.2 0.26 25.44 3

4 10 2 748.922 4 2.2 0.58 39.1 5

5 2 2 701.381 4 0.9 0.69 39.05 5

6 25 2 595.825 4 1.5 0.78 38.98 5

7 6 2 503.309 4 2.1 0.51 37.89 4

8 19 2 584.086 4 -0.2 0.45 37.03 4

9 5 1 895.504 3 3.2 0.66 36.78 4

10 6 2 411.49 4 -1.6 0.69 36.16 3

11 13 2 608.73 5 2.3 0.53 35.3 3

12 8 2 903.184 3 4.7 0.59 34.33 4

13 2 1 493.893 5 0 0.38 34.03 2

14 4 2 582.057 4 -0.9 0.52 33.88 4

15 6 2 969.827 3 2.6 0.46 33.17 3

16 11 2 894.688 4 2.2 0.44 33.01 3

17 7 2 817.14 3 0.3 0.61 32.82 1

18 5 2 900.465 5 5.7 0.59 32.47 9

19 2 1 902.5 3 2.4 0.61 31.8 3

20 1 1 969.798 4 -0.7 0.6 31.08 3

21 1 1 756.398 4 -0.3 0.35 30.77 3

22 4 2 1151.954 3 4 0.55 29.99 6

23 9 2 471.668 5 -0.2 0.18 29.24 1

24 3 1 577.313 4 1.1 0.26 29.22 0

25 4 2 1208.612 3 4.7 0.37 29.07 7

26 8 2 1063.536 4 6.1 0.37 28.74 3

27 2 2 539.061 4 -3.5 0.41 28.64 3

28 2 1 487.036 4 -1.1 0.46 27.98 4

29 1 1 583.801 4 -3.6 0.52 27.4 3

30 4 2 868.238 5 3.4 0.3 27.01 0

31 1 1 617.115 4 1.3 0.4 26.71 3

32 4 2 773.889 4 4.2 0.14 25.53 3

33 1 1 618.356 4 3.6 0.51 24.52 1

34 4 2 601.124 5 0.7 0.08 23.76 3

35 4 2 746.807 5 2.7 0.27 23.23 1

36 2 1 645.331 5 -1.3 0.14 22.89 2

37 2 1 923.467 4 2.1 0.28 22.05 3

38 1 1 770.026 5 5.2 0.3 21.63 2

39 1 1 494.563 4 -2.9 0.57 37.52 4

40 1 1 693.867 4 2 0.38 30.29 3

41 1 1 546.061 4 3.1 0.45 29.68 4

42 44 13 846.467 4 2.1 0.5 37.47 6

43 9 6 706.873 4 5.2 0.69 34.05 3

44 5 4 1112.588 4 6.3 0.51 24.77 3

45 5 3 776.23 5 4.2 0.59 34.99 7

46 2 1 744.375 4 5 0.43 30.7 6

47 69 14 689.384 4 2.6 0.69 40.82 5

48 1 1 802.401 4 0.3 0.61 35.05 8

49 4 3 649.34 4 1.7 0.5 32.89 1

50 1 1 782.179 4 4.8 0.35 32.43 8

51 3 2 882.872 5 5.1 0.54 31.38 2

52 2 2 477.776 4 -0.3 0.38 29.6 2

53 4 3 800.999 5 1.1 0.49 27.81 7 2cqy 27.6 29.8

54 2 1 1297.076 5 7 0.48 27.73 6

80  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

55 4 2 1257.124 4 6.5 0.39 33.94 7

56 8 4 1005.898 5 3.6 0.56 40.37 7

57 46 8 602.687 3 -1.1 0.34 39.14 5

58 10 2 455.762 4 -0.9 0.48 36.94 4

59 1 1 807.185 4 1.3 0.32 28.59 5

60 13 5 634.526 5 5.6 0.57 39.92 6 1hjo 5.3 5.1

61 10 8 870.976 4 6.4 0.48 30.48 4 1hjo 15.5 19.8

62 3 3 692.389 4 -0.9 0.35 29.21 4

63 2 1 695.888 4 2.9 0.29 27.4 5 1hjo 4.8 4.9

64 13 7 540.301 4 3.2 0.72 43.44 5

65 1 1 685.094 4 1.6 0.42 31.65 3

66 1 1 536.795 4 -0.1 0.59 25.86 3

67 2 1 518.042 4 -2.6 0.64 38.56 4 1hjo 9.6 17.4

68 3 3 1014.848 3 -3.6 0.38 33.14 6

69 10 5 913.119 3 -1.9 0.4 30.82 2

70 18 7 447.743 4 -1.5 0.5 39.87 5

71 1 1 401.021 5 5.1 0.36 32.14 3

72 18 1 791.122 3 2.9 0.58 43.87 7

73 1 1 950.829 3 2.8 0.45 42.49 8 1gk7 24.4 34.2

74 18 1 784.688 4 0.9 0.48 35.83 7

75 5 1 756.401 4 3.3 0.39 34.72 5

76 2 1 437.999 4 -4 0.79 40.13 4

77 1 1 610.373 4 0.5 0.84 32.25 3

78 8 5 467.536 4 -1.7 0.42 31.51 4 3iuc 10.8 14.5

79 3 1 551.901 5 1.6 0.33 31.39 5 3fzf 4.8 5.9

80 3 2 695.367 5 5.8 0.51 20.69 3 3fzf 18.8 22.7

81 1 1 866.455 4 4.5 0.21 20.21 2

82 3 2 629.591 4 2 0.16 23.93 3

83 12 3 507.036 4 -0.5 0.71 37.3 3 3fzf 9.7 17.5

84 3 2 451.249 4 -1.9 0.69 35.7 4

85 1 1 447.248 4 -1.3 0.34 34.28 4

86 31 5 536.795 4 0.2 0.73 40.99 5

87 1 1 646.88 4 -0.7 0.32 26.89 4 1zwv 15.9 29.6

88 6 2 602.352 5 2.5 0.63 37.73 4

89 3 1 575.077 4 0.8 0.42 33.11 3 1zwv 4.5 5.5

90 23 10 667.731 3 3.8 0.43 39.15 6

91 19 7 843.93 4 -0.9 0.37 35.33 4

92 12 7 528.802 4 1.8 0.38 34.04 3

93 37 7 598.533 5 5.7 0.32 31.62 3 3bg3 19.4 22

94 11 8 690.196 5 2.4 0.69 28.53 3

95 3 2 523.33 4 1.1 0.63 39.9 4 3bg3 19.3 25.3

96 17 7 405.456 5 2.2 0.44 39.11 5

97 1 1 629.116 4 1.9 0.51 37.31 5

98 27 7 587.091 4 1.3 0.41 35.8 4

99 28 6 405.455 5 0.7 0.21 35.75 4

100 2 1 485.707 5 2.5 0.57 35.57 3

101 5 2 572.323 5 4.4 0.5 35.33 4

102 2 1 570.082 4 1.8 0.48 34.25 5 3bg3 19.1 31.4

103 19 8 639.354 5 1.8 0.36 33.96 4

104 1 1 777.64 5 3.8 0.48 33.55 8 3bg3 14.9 18.4

105 8 6 1063.808 4 2.8 0.68 33.55 4

106 2 2 431.514 4 3.1 0.39 33.14 4

107 10 4 422.466 5 1.5 0.33 32.98 3

108 15 6 946.994 4 3.2 0.41 31.27 7

109 5 2 438.748 6 0.2 0.43 30.98 2

110 2 2 423.521 4 2.3 0.51 30.16 3 3bg3 12 21.8

111 4 2 407.504 4 -0.3 0.27 29.03 3 3bg3 34.9 56.2

112 2 1 552.322 5 0.8 0.36 28.65 3

113 17 7 627.941 5 4.3 0.22 28.47 2

114 1 1 478.889 5 1.8 0.45 27.82 2

115 1 1 627.556 5 0.7 0.4 26.77 4

116 1 1 551.683 3 1.8 0.37 26.1 4 3bg3 20.9 36.4

117 2 1 644.623 4 2.4 0.2 25.35 2

118 1 1 621.336 6 6 0.26 22.31 2

119 1 1 632.133 5 3 0.34 22.26 3

120 1 1 721.187 5 7 0.37 20.34 3

121 1 1 682.065 3 2.6 0.63 38.94 4 3bg3 15.4 20.8

122 37 6 469.874 5 0.9 0.55 38.73 4

123 10 5 590.54 5 6.5 0.64 38.33 3

124 33 6 879.23 4 2.5 0.48 36.39 5

125 8 5 610.929 5 2.8 0.46 36.29 4

126 19 9 550.065 4 0.6 0.4 35.64 4

127 5 3 381.24 4 -0.2 0.54 34.89 3 3bg3 13.2 16.4

128 11 4 552.324 5 4 0.45 34.26 3

129 17 4 422.466 5 0.7 0.35 34.12 4

130 8 3 469.874 5 0.5 0.57 33.42 4

131 4 4 690.203 5 3.8 0.4 33.21 3 3bg3 14.5 24.2

132 15 5 613.737 5 5 0.35 32.11 6

81  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

133 10 5 832.632 5 3.9 0.37 31.76 6

134 1 1 484.873 5 5.9 0.26 30.08 4

135 3 2 423.017 4 2.1 0.52 30 4 3bg3 26.9 44

136 2 2 621.335 6 5.2 0.3 29.69 3

137 11 7 721.376 5 6.7 0.31 27.2 4

138 33 8 574.33 4 -1.2 0.37 39.93 4

139 59 11 694.74 3 2.4 0.6 39.48 3 3bg3 22.9 25

140 95 13 595.594 4 0.7 0.29 38.45 4

141 45 8 551.513 5 2.7 0.29 35.93 3

142 25 8 394.229 5 1.6 0.28 34.91 3

143 9 3 522.798 6 -0.9 0.42 34.71 3

144 6 4 394.228 5 -0.2 0.36 33.54 1

145 10 5 522.299 4 5 0.24 33.5 2 3bg3 13.8 16.9

146 10 3 522.798 6 -0.9 0.49 32.97 3

147 18 8 570.111 5 1.8 0.36 32.79 3

148 10 7 377.219 5 3.2 0.21 31.62 3

149 11 4 391.73 6 0.3 0.15 30.79 3

150 1 1 761.169 4 4.6 0.25 24.37 3 3bg3 27.5 34.2

151 3 3 471.271 4 1.2 0.13 20.05 3

152 28 9 895.226 4 1.2 0.66 39.46 7 TRiC 10.3 12.8

153 9 5 655.125 4 0.5 0.43 39.26 5 TRiC 8 8.7

154 2 1 823.868 5 5.6 0.49 26.7 4 TRiC 8.3 9.7

155 1 1 801.688 4 -1.4 0.2 21.37 5 TRiC 18.7 30.1

156 4 2 1006.852 3 0.8 0.64 39.35 9 TRiC 19.7 27.1

157 32 10 612.343 4 -0.9 0.42 35.06 3 TRiC 11.1 16.5

158 1 1 619.832 4 3.9 0.31 23.12 4 3dw8 24 40.2

159 22 8 563.579 4 3.4 0.53 39.78 4 3dw8 10.7 21.8

160 10 5 670.06 3 4.8 0.5 38.42 7 3dw8 39.3 49.9

161 4 4 535.632 6 1.6 0.41 31.43 5 3dw8 30.5 64.8

162 34 12 640.369 3 2.5 0.39 31.12 3 3dw8 8.7 9.3

163 5 2 550.07 4 4.3 0.47 30.87 5 3dw8 25.9 29.8

164 16 9 600.658 6 2.5 0.4 29.21 6 3dw8 16 51.8

165 1 1 522.813 4 4.2 0.32 27.56 4 3dw8 30.3 33.7

166 83 17 440.011 4 2.9 0.72 40.45 3 3dw8 15 19.4

167 34 18 713.992 5 4.5 0.56 38.57 7 3dw8 12.2 31.3

168 5 3 1285.404 4 5.1 0.52 30.15 4 3dw8 11.2 17.7

169 9 4 1253.912 4 6.3 0.47 26.94 4 3dw8 12.8 16.5

170 2 2 817.04 5 -1.3 0.39 26.87 7 3dw8 20.4 47.9

171 139 15 1091.612 3 5.6 0.59 40.78 10 3dw8 16.9 20.2

172 51 16 685.568 5 2.5 0.59 37.8 5 3dw8 18.8 55.6

173 14 6 938.031 4 1.2 0.5 30.67 6 3dw8 14.8 20.7

174 12 7 866.14 3 -3.2 0.34 30.49 8 3dw8 9.5 19.6

175 4 3 1131.396 5 6.9 0.76 28.57 4 3dw8 14.5 19.3

176 6 4 832.169 4 2.3 0.41 30.82 4 3dw8 14.1 20.1

177 4 3 600.312 6 2.6 0.27 28.7 5 3dw8 35.1 45.6

178 25 7 529.301 4 -0.4 0.56 40.34 6 3dw8 24.9 43.3

179 65 12 796.93 4 3.9 0.57 40.03 6 3dw8 18 20.7

180 11 3 572.556 4 -1.7 0.19 34.36 5 3dw8 36 46.9

181 26 10 763.767 3 2 0.55 38.83 8 3dw8 16.2 21.4

182 25 9 807.767 3 -0.4 0.61 38.46 6 3dw8 9.1 11.6

183 12 6 553.803 6 1.1 0.48 36.78 5 3dw8 42.1 73

184 81 18 768.428 3 -1.7 0.5 36.46 6 3dw8 15.6 19.5

185 23 9 680.36 3 -1.2 0.3 34.24 4 3dw8 21.7 42.6

186 1 1 838.114 6 -1 0.4 23.36 2 3dw8 25.4 33.5

187 4 1 675.84 4 1.3 0.24 30.39 6 3dw8 17.4 36.4

188 619.832 4 3.9 0.31 23.12 4 3dw8 23.4 40

189 14 3 664.388 3 4.4 0.54 36.14 7 3dw8 38.6 48.6

190 2 1 1077.585 5 5 0.31 31.41 7 3dw8 11.9 15.2

191 522.813 4 4.2 0.32 27.56 4 3dw8 30.9 35

192 18 2 489.68 5 2.3 0.58 40.3 5 3dw8 16 21.3

193 17 2 675.723 3 2.5 0.53 39.72 6 3dw8 25 29.6

194 6 2 826.98 4 2.1 0.58 37.92 6 3dw8 12.7 36.9

195 3 2 686.641 4 6.2 0.36 36.64 6 3dw8 13.6 23.8

196 3 1 572.303 4 1.1 0.29 33.5 6 3dw8 36.4 48

197 1 1 800.921 4 4.2 0.42 33.45 9 3dw8 20 24

198 4 2 1052.259 3 4.1 0.47 33.27 6 3dw8 14.1 47.7

199 4 2 617.357 3 3.4 0.44 32.67 3 3dw8 33.4 37

200 14 2 483.785 4 0.6 0.4 32.67 4 3dw8 30.9 35

201 4 2 650.883 4 2.7 0.59 30.96 0 3dw8 33.5 37

202 1 1 1391.408 3 2.2 0.53 30.88 4 3dw8 15.5 24.2

203 5 2 731.807 5 4.4 0.47 28.07 1 3dw8 15.9 52.7

204 3 1 616.565 4 0.7 0.15 24.92 2 3dw8 25.1 50.2

205 440.011 4 2.9 0.72 40.45 3 3dw8 14.5 20.3

206 15 5 906.003 4 1.9 0.38 28.84 3 3dw8 11.7 30.2

207 27 8 730.899 4 -0.5 0.47 38.57 6 3dw8 16.1 19

208 1 1 529.047 4 0.9 0.43 31.56 4 3dw8 24.5 43.1

209 2 2 696.787 5 3.9 0.44 21.44 2 3dw8 18.5 55.1

210 768.428 3 -1.7 0.5 36.46 6 3dw8 15.4 19.3

82  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

211 2 1 675.03 3 0.2 0.22 33.81 4 3dw8 19.4 40.2

212 5 3 415.741 4 -0.8 0.65 43.41 3 TRiC 5.3 5.7

213 31 9 649.123 4 4.9 0.56 40.1 5 TRiC 6.9 7.4

214 2 1 479.548 4 2.5 0.33 38.61 4 TRiC 3.8 4.1

215 29 8 422.755 4 -1.6 0.47 41.89 4 TRiC 12.2 17.8

216 7 4 571.32 4 0.4 0.57 39.8 5 TRiC 42.4 53.7

217 150 16 389.822 5 -0.8 0.31 39.28 4 TRiC 11.7 17.2

218 33 9 472.532 4 -1.6 0.59 37.58 4 TRiC 5.3 5.7

219 21 8 534.046 4 2.5 0.36 36.27 4 TRiC 9.4 9.5

220 116 9 678.398 4 5.3 0.54 34.46 5 TRiC 14.1 22

221 17 7 476.676 5 2.8 0.49 31.8 3 TRiC 14.8 16.7

222 5 3 532.893 5 -0.4 0.3 31.28 5 TRiC 11 17.4

223 8 4 567.742 7 -2 0.7 29.15 4 TRiC 10.6 14.4

224 4 3 648.138 5 4.6 0.3 27.98 4 TRiC 17 28.6

225 13 5 620.33 5 -1.1 0.54 35.03 7 TRiC 27.3 34.3

226 1 1 917.854 3 0.3 0.43 27.16 7 TRiC 9.7 14.6

227 11 7 487.025 4 -1.7 0.24 26.83 2 TRiC 5.3 5.3

228 2 2 808.842 5 -0.4 0.3 20.27 4 TRiC 9.2 9.7

229 3 2 662.696 3 0.9 0.52 32.51 4 TRiC 11.1 20.6

230 5 2 670.613 4 1 0.46 38.66 4 TRiC 21.6 31.7

231 24 8 1102.975 3 2.4 0.53 36.66 5 TRiC 20.4 24.8

232 4 2 682.976 5 6.3 0.6 32.17 2 TRiC 10 10.9

233 2 2 682.973 5 2.1 0.4 29.74 1 TRiC 9.7 13.4

234 6 3 625.61 4 5.2 0.61 37.9 4 TRiC 12 13.5

235 10 4 613.328 4 2.5 0.46 36.39 6 TRiC 16.2 24.8

236 4 4 760.011 5 1.2 0.63 35.39 7 TRiC 16 22.7

237 2 2 771.608 5 4.1 0.39 31.13 4 TRiC 10.4 14.1

238 4 3 676.182 5 2.3 0.35 24.64 4 TRiC 17.6 23.4

239 13 4 475.28 4 -0.5 0.66 42.26 7 TRiC 11 15.2

240 5 2 643.359 3 -1.3 0.69 40.34 7 TRiC 9.5 16.5

241 100 12 447.26 4 -2 0.58 39.86 5 TRiC 23.5 25.9

242 3 1 571.816 4 -2.2 0.54 35.88 3 TRiC 7.9 8.6

243 23 7 453.528 4 -0.6 0.55 34.3 4 TRiC 17.9 21.5

244 2 2 697.366 3 -3.2 0.33 26.4 3 TRiC 13.1 17.5

245 13 6 840.121 3 -0.3 0.7 38.06 6 TRiC 10.3 16.1

246 3 2 752.651 4 6 0.28 30.63 2 TRiC 14.9 29.9

247 43 12 565.105 5 1.5 0.45 42.54 5 TRiC 18.3 22.3

248 55 11 711.198 5 3.8 0.5 38.93 3 TRiC 14.4 17.7

249 94 11 1064.277 3 4.7 0.49 38.42 6 TRiC 13.8 18.2

250 53 8 514.269 4 0.7 0.77 42.41 5 TRiC 5.3 6.3

251 110 8 810.688 4 2.2 0.67 39.66 6 TRiC 5.3 5.3

252 1 1 741.586 5 3.1 0.64 34.36 2 TRiC 18.3 33

253 4 4 830.481 4 1.2 0.48 26.63 5 TRiC 11.5 17.7

254 9 4 574.316 4 -2.2 0.58 40.85 4 TRiC 18.3 35.2

255 2 1 797.179 4 -1.5 0.39 34.46 7 TRiC 15.4 32.9

256 17 3 793.44 3 -0.5 0.43 35.56 6 TRiC 15.9 20.5

257 18 6 752.644 4 -3.4 0.39 34.79 3 TRiC 12.1 27.7

258 4 2 563.546 4 -1.4 0.42 34.33 3 TRiC 12.1 21.4

259 45 8 719.859 4 -2.4 0.59 33.78 2 TRiC 11.6 17.6

260 2 1 880.953 4 1.4 0.4 31.52 2 TRiC 14.3 30.8

261 2 2 734.717 3 -0.4 0.43 30.59 2 TRiC 22.8 24.9

262 5 1 734.06 3 -2.3 0.38 29.09 5 TRiC 17.1 29.5

263 1 1 550.796 4 -3.6 0.34 28.01 1 TRiC 19.6 25.9

264 2 1 543.964 3 -2.6 0.3 26.71 1 TRiC 16.9 24.5

265 2 1 816.646 5 2.3 0.34 26.51 3 TRiC 19.4 29.5

266 1 1 760.371 4 -1.7 0.25 20.08 2 TRiC 22.9 25.7

267 1 1 1161.573 4 0.8 0.43 26.07 1 TRiC 17.4 19.8

268 1 1 1241.865 4 0.5 0.46 24.45 7 TRiC 17.2 33

269 84 14 653.621 4 3.4 0.44 40.05 6 TRiC 12.6 18.1

270 7 2 986.872 3 -2.4 0.56 36.98 8 TRiC 17 18.4

271 2 1 599.13 5 -3.9 0.27 28.91 3 TRiC 17.6 19.1

272 4 2 694.182 5 -3 0.38 32.68 3 TRiC 17.7 22.4

273 2 2 1086.166 5 3.5 0.43 26.62 0 TRiC 11.5 20.3

274 6 2 679.16 4 4.3 0.52 36.43 6 TRiC 5.8 5.9

275 2 2 1089.828 4 6.7 0.27 23.15 1 TRiC 18.3 20.3

276 9 3 625.348 4 -1.8 0.5 35 3 TRiC 20.1 29.2

277 8 4 594.925 5 -3.7 0.46 33.12 3 TRiC 10.2 17.1

278 10 4 510.662 5 -3.8 0.58 40.54 8 TRiC 10 18.4

279 15 7 844.207 4 1.4 0.69 32.91 3 TRiC 21.3 32.3

280 5 2 778.817 5 2.1 0.35 29.45 5 TRiC 16.6 20.2

281 22 9 1223.983 3 2.2 0.56 37.41 7 TRiC 8.2 8.9

282 8 5 756.623 5 5.8 0.4 32.49 7 TRiC 17.1 25

283 17 3 541.041 4 2.8 0.52 39.09 5

284 2 1 786.403 5 2.2 0.44 24.97 0

285 289 5 844.451 3 -0.4 0.55 44.04 6 3fga 11.9 18.3

286 51 9 1014.891 3 5.4 0.68 43.46 4 3dw8 10.4 18.9

287 10 3 672.111 4 3.5 0.41 27.12 6 3dw8 31.5 39.4

288 3 2 712.62 4 1.6 0.27 23.08 4 3dw8 28.7 44.7

83  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

289 18 9 719.375 4 0.6 0.46 36.64 6 3dw8 31.5 36.8

290 18 7 654.87 4 -1.3 0.47 36.3 4 3dw8 18 21.8

291 3 2 672.11 4 2.6 0.28 24.32 3 3dw8 20 24.4

292 2 2 498.48 5 0.8 0.52 35.82 4 3dw8 18 20.8

293 11 6 498.48 5 1.5 0.53 35.43 3 3dw8 18 21.8

294 4 3 439.763 4 0.2 0.62 34.11 5 3dw8 22.4 29.3

295 4 2 894.14 3 2.9 0.45 32.02 5 3dw8 6.9 8

296 4 2 670.858 4 3.3 0.57 31.01 5 3dw8 10.4 16.5

297 2 2 719.375 4 0.5 0.4 30.62 4 3dw8 18.7 23.5

298 10 4 400.738 4 1.7 0.57 30.33 3 3dw8 9.7 12.8

299 114 11 624.101 4 0.1 0.88 42.38 4 3dw8 12.9 17.6

300 1 1 384.42 5 -1.1 0.7 33.18 4 3dw8 17.4 26.2

301 8 4 593.712 5 0.4 0.32 30.61 4 3dw8 27.7 40.8

302 8 4 803.411 5 2.6 0.29 29.09 6 3dw8 22.3 26.6

303 41 2 444.442 5 1.1 0.63 41.55 4 1cmi-2 12.1 17.8

304 69 17 825.787 3 2.6 0.41 33.52 4 3fga 10.7 13.8

305 136 7 630.089 4 3.4 0.48 40.42 3 3fga 12 16.6

306 9 7 1051.527 3 0.2 0.53 33.39 4 3fga 14.6 20.2

307 1 1 1392.113 5 5.1 0.34 24.64 3 3fga 9.1 9.7

308 2 1 645.032 3 1.7 0.28 30.74 2

309 7 4 517.561 4 1.3 0.4 31.2 2

310 3 3 532.81 4 2.1 0.4 29.23 3

311 3 3 599.615 4 3.5 0.17 21.43 5

312 7 6 435.746 4 -3 0.18 27.05 3

313 9 6 503.783 4 -2.5 0.28 27.55 3

314 6 3 879.665 5 3.9 0.39 30.62 4

315 1 1 615.745 5 3.1 0.37 29.78 4

316 3 2 615.744 5 2 0.39 29.64 4

317 1 1 612.604 4 1.9 0.6 28.15 5

318 1 1 709.557 5 4 0.44 23.04 4

319 6 5 845.811 5 1.8 0.54 33.84 3

320 22 5 720.88 4 3.3 0.34 30.14 4

321 2 2 759.366 5 2.2 0.39 24 3

322 9 5 670.084 4 -3.7 0.27 25.09 4

323 43 2 686.763 5 0.7 0.48 43.25 5

324 26 3 576.744 5 3.7 0.42 42.17 5

325 3 1 723.9 4 4.7 0.7 41.7 3

326 8 2 652.495 6 -0.7 0.61 41.25 5

327 8 3 755.96 5 0.8 0.45 41.05 3

328 18 3 778.145 4 2.5 0.61 40.72 4

329 22 3 532.868 5 4.1 0.45 40.61 4

330 9 2 602.724 5 3.5 0.69 40.41 2

331 5 2 677.904 4 2.1 0.33 39.47 6

332 9 3 636.576 4 -0.4 0.42 39.36 5

333 14 3 519.27 5 4.3 0.23 38.4 4

334 2 1 602.917 5 4.1 0.53 38.29 2

335 15 3 545.131 6 4.8 0.44 37.97 3

336 4 2 532.562 4 2.4 0.35 37.66 4

337 22 3 832.866 5 -0.3 0.51 37.5 5

338 2 2 884.242 5 5.6 0.29 37.29 5

339 11 3 892.125 3 5 0.41 36.85 5

340 3 2 511.307 4 2.3 0.29 36.3 2

341 7 2 980.272 5 4.9 0.6 36.19 2

342 3 2 390.428 5 0.6 0.08 35.66 4

343 86 3 465.105 6 1.9 0.31 35.51 5

344 43 4 780.427 5 4.8 0.59 34.84 3

345 8 3 628.675 6 5.1 0.42 34.78 4

346 3 2 1007.482 5 5.5 0.5 33.62 3

347 9 3 603.862 4 5 0.35 33.43 4

348 2 1 923.081 5 6.9 0.45 33.17 1

349 4 3 785.451 5 7 0.67 32.73 4

350 5 2 592.345 4 4.8 0.26 32.33 1

351 2 1 710.62 4 1.2 0.28 32.12 5

352 2 2 912.677 4 3.5 0.18 31.73 5

353 4 2 659.996 6 4.6 0.28 31.34 5

354 2 1 796.792 3 3 0.38 30.16 4

355 14 4 971.158 6 4.4 0.42 30.15 2

356 2 1 688.512 6 5.5 0.42 30.09 4

357 3 2 606.13 5 3.3 0.24 29.27 5

358 3 2 1046.999 6 6.5 0.52 28.39 3

359 9 3 919.301 6 6.4 0.38 28.37 1

360 31 6 693.978 5 0.8 0.29 27.59 6

361 79 10 750.134 4 1.4 0.5 34.31 4

362 10 5 1057.014 4 3.6 0.54 32.01 5

363 12 4 1146.323 4 3.1 0.42 30.72 5

364 9 4 732.558 5 2.5 0.29 30.5 4

365 2 2 910.413 5 3.2 0.36 33.62 5

366 30 6 756.623 5 5.2 0.51 32.23 3

84  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

367 15 5 1225.085 4 2.6 0.38 31.2 5

368 30 5 423.744 4 -1 0.28 36.82 3

369 5 4 936.032 5 3.2 0.45 31.94 5

370 85 3 616.115 4 -1.4 0.14 35.01 4

371 11 3 589.123 5 -1.5 0.24 34.12 4

372 23 3 603.86 4 0.6 0.39 33.08 3

373 4 1 394.492 4 4.5 0.2 32.76 3

374 7 1 553.054 4 -3.2 0.62 32.41 3

375 1 1 794.922 4 1 0.36 31.75 6

376 3 2 862.45 4 5 0.55 30.1 5

377 36 3 720.879 4 0.9 0.35 29.45 3

378 8 3 536.057 4 -2.6 0.55 29.32 2

379 3 1 1299.664 4 3.7 0.52 29.15 0

380 1 1 624.376 3 0.5 0.13 27.22 4

381 7 3 445 4 1.4 0.38 27.11 3

382 3 3 650.188 7 3.5 0.28 23.27 2

383 1 1 603.713 5 -0.2 0.23 20.62 3

384 13 5 636.105 4 6.1 0.41 38.16 6 TRiC 11.9 17.6

385 24 6 568.722 5 3.3 0.43 41.57 4 TRiC 23.6 27.5

386 55 7 585.561 4 -3.6 0.48 40.8 6 TRiC 9.6 9.6

387 31 10 855.459 3 -1.3 0.41 40.69 6 TRiC 11.5 12.3

388 25 6 588.521 5 1.8 0.47 39.79 5 TRiC 22.6 29.2

389 14 5 560.813 4 0.3 0.51 39.24 4 TRiC 16.6 23

390 15 5 906.99 4 -0.4 0.49 38.59 6 TRiC 12.2 19

391 12 7 732.429 5 0.5 0.57 36.12 5 TRiC 18.8 23.9

392 12 5 585.561 4 -3.2 0.49 35.64 3 TRiC 5.9 6.1

393 12 4 470.025 4 4.8 0.5 35.56 4 TRiC 13.8 15.8

394 1 1 376.22 5 1 0.45 35.47 3 TRiC 17.3 19.6

395 33 10 509.084 5 2.9 0.41 34.82 4 TRiC 9.8 18.6

396 1 1 490.602 6 1.6 0.41 30.64 2 TRiC 19.4 26.8

397 10 3 690.98 5 2.3 0.39 36.36 5 TRiC 20.3 24.7

398 7 5 869.794 3 3.3 0.31 30.68 7 TRiC 8.9 10.3

399 5 3 711.187 5 0.6 0.59 27.92 2 TRiC 23.1 28.2

400 6 3 560.1 5 0.3 0.27 23.92 1 TRiC 21.6 23.9

401 3 1 570.337 7 0.7 0.48 21.21 4 TRiC 17 53.7

402 32 6 886.488 4 -1.8 0.53 38.14 7 TRiC 10 10.6

403 3 1 1003.261 4 -2.4 0.54 34.71 10 TRiC 16 28.2

404 2 2 652.182 5 -0.2 0.3 28.58 4 TRiC 17.1 54.4

405 4 4 920.011 4 -1.4 0.33 26.49 3 TRiC 15.8 20.2

406 23 6 782.954 4 3 0.54 40.52 8 TRiC 15 23.3

407 28 7 1011.559 3 1.4 0.84 39.18 8 TRiC 14 18

408 63 15 793.76 3 -3.3 0.61 38.74 7 TRiC 5.2 6.4

409 28 7 807.469 4 -0.6 0.38 35.33 6 TRiC 18 21.6

410 1 1 899.728 4 3.1 0.47 31.08 7 TRiC 14.4 19.6

411 1 1 991.016 4 1.6 0.42 27.93 3 TRiC 8.7 9.1

412 6 2 898.238 4 1.4 0.34 27.32 6 TRiC 16.7 26.7

413 4 2 510.275 5 1.2 0.51 25.36 2 TRiC 14.1 19.1

414 1 1 812.901 4 4 0.34 35.07 7

415 42 4 940.727 4 6.4 0.58 34.38 6 2e50 10.1 16.1

416 2 1 626.003 3 2.2 0.41 34.29 4

417 21 3 716.719 3 1.6 0.29 33.49 6

418 2 1 519.076 4 -0.2 0.57 34.9 1

419 3 1 590.295 4 -0.9 0.51 28.38 4

420 16 4 797.095 3 2.8 0.49 41.72 5

421 14 1 804.445 3 -0.1 0.42 33.8 4

422 13 1 735.158 4 0.6 0.45 26.78 5

423 2 1 852.823 3 5 0.47 26.23 4

424 1 1 739.128 4 -3.8 0.35 25.43 4

425 1 1 790.653 4 1.5 0.18 24.35 2

426 30 8 1130.96 3 4.3 0.44 37.76 6

427 8 2 965.526 3 5.1 0.39 37.26 6

428 12 6 526.306 4 0.9 0.63 35.94 3

429 17 8 844.95 4 1.7 0.42 32.56 3

430 13 5 927.524 3 1.9 0.61 41.64 7

431 5 1 630.352 4 0.4 0.42 36.96 4

432 1 1 465.655 5 -0.4 0.48 35.83 5

433 5 4 876.966 4 2.7 0.45 35.38 5

434 6 2 416.842 5 1.1 0.46 34.4 4

435 1 1 642.626 4 1.5 0.26 30.04 6

436 40 9 678.742 3 1 0.59 38.88 5

437 13 6 905.817 3 0.3 0.37 33.57 6

438 11 5 715.642 4 1.1 0.37 32.91 6

439 5 3 598.33 4 2 0.55 30.39 3

440 1 1 551.501 5 0.8 0.33 26.5 4

441 1 1 710.578 4 -0.4 0.43 35.22 6

442 12 5 771.896 4 -1.6 0.38 35 6

443 4 2 700.841 4 0.2 0.58 31.31 5

444 11 7 845.477 3 1.3 0.5 38.27 5

85  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

445 2 1 967.477 3 2.8 0.49 33.45 5

446 5 3 880.779 3 2.9 0.25 33.11 5

447 3 2 703.649 4 1.9 0.42 31.99 2

448 6 3 701.035 3 0.9 0.19 31 7

449 2 1 439.263 4 -0.7 0.63 27.91 4

450 183 10 574.79 6 1.6 0.48 37.95 5 3fga

451 4 2 551.066 4 0.9 0.52 35.57 5 3fga 6.2 7.1

452 9 3 632.089 4 0.1 0.48 35.2 3 3fga 10.6 11.7

453 18 5 756.383 4 0.2 0.45 34.48 7 3fga 20.7 23.3

454 25 7 396.223 5 2 0.44 33.8 3 3fga

455 10 4 756.383 4 -0.9 0.45 33.09 6 3fga 22.8 25.8

456 5 4 647.605 4 -0.3 0.39 32.65 3 3fga

457 3 2 842.455 3 6.8 0.25 27.35 5 3fga 8.4 9.1

458 3 2 531.08 4 1.3 0.7 43.61 6 3fga 26.7 41.7

459 92 9 758.088 3 2.5 0.74 37.21 4 3fga

460 10 2 575.316 4 0 0.58 37.02 3 3fga

461 24 2 854.701 4 4.1 0.56 36.78 5 3fga 14.5 16.8

462 4 2 677.629 4 1.8 0.43 35.64 5 3fga

463 3 2 475.794 4 0.1 0.78 33.95 5 3fga 14.1 18.6

464 3 2 905.678 5 5.2 0.68 33.41 3 3fga 11.4 17.2

465 1 1 692.427 4 1.2 0.34 33.01 4 3fga 12.7 15.2

466 3 2 615.066 4 3.1 0.21 32.6 4 3fga 34.7 40.3

467 1 1 601.064 4 1.1 0.08 21.03 2 3fga

468 8 6 518.286 5 0.6 0.64 34.29 4 3fga

469 1 1 594.584 4 -1 0.35 33.85 5 3fga

470 710.148 4 2.4 0.48 33.68 4 3fga 9.7 18.7

471 92 9 480.873 5 -1 0.26 31.08 4 3fga

472 22 2 576.504 5 0.8 0.71 37.39 5 3fga

473 8 2 500.292 4 1.7 0.46 37.35 3 3fga 13.4 23.4

474 1 1 584.34 4 0.9 0.56 37.22 7 3fga 14.6 23.9

475 3 2 475.793 4 -2.2 0.73 36.11 3 3fga 9.1 14.4

476 7 2 809.748 3 0.7 0.52 34.89 6 3fga

477 11 3 508.529 4 -0.3 0.48 31.29 4 3fga 12.5 14.3

478 2 2 818.036 5 3.1 0.36 29.15 3 3fga 13.5 15.1

479 5 1 1022.041 4 3.7 0.42 28.51 3 3fga 14.2 17.5

480 1 1 752.884 4 -0.9 0.09 20.43 1 3fga 17.1 24.9

481 2 1 600.596 4 -0.1 0.49 35.45 7 3fga 17.4 30.2

482 6 3 853.707 4 5.9 0.57 33.31 3 3fga 16.7 21.9

483 3 2 742.399 4 -1.4 0.53 29.21 3 3fga 18.5 23.1

484 5 2 903.827 3 3.2 0.43 30.89 4 2vn9 15.1 16.6

485 2 1 538.814 4 -1.6 0.28 30.73 4 2vn9, 2v7o 20.2 35.5

486 2 2 552.323 4 0.7 0.27 23.05 3 2vn9,

2v7o, 3bhh 14.7 25.1

487 63 8 959.212 3 0.6 0.41 40.8 7 3fga

488 28 9 794.775 3 2.7 0.41 39.28 6 3fga

489 4 4 760.624 4 2.8 0.45 38.23 4 3fga 19.1 25

490 15 4 608.699 5 -0.1 0.72 36.56 5 3fga 16.6 19.9

491 10 3 534.523 4 1.8 0.52 36.43 3 3fga 12.4 18.7

492 4 2 554.582 4 -0.7 0.39 35.85 5 3fga

493 2 1 589.804 4 0 0.6 34.21 3 3fga

494 3 1 710.148 4 2.4 0.48 33.68 4 3fga 9.6 12.4

495 4 2 589.943 5 -0.6 0.43 33.26 2 3fga

496 6 2 851.195 4 1.8 0.5 33.24 2 3fga 14.7 17.1

497 15 6 579.588 4 2.9 0.63 32.97 0 3fga

498 8 3 469.539 4 0.9 0.64 32.74 6 3fga

499 2 1 456.672 5 2.5 0.37 32.61 5 3fga

500 191 12 1009.3 4 3.4 0.48 31.92 5 3fga 20.8 24.2

501 1 1 753.813 5 -1.6 0.47 31.61 7 3fga

502 6 2 657.568 5 4.5 0.56 31.22 7 3fga

503 1 1 773.436 3 3.4 0.38 30.53 5 3fga

504 9 3 696.66 4 3.3 0.3 27.36 3 3fga

505 1 1 526.308 5 0.9 0.27 24.53 1 3fga

506 1 1 686.126 4 5.6 0.14 21.67 1 3fga

507 13 6 834.177 4 5.2 0.59 34.02 5 3fga 21 24.5

508 14 5 1169.837 4 1.7 0.51 30 5 3fga

509 18 5 514.556 4 1.2 0.24 35.37 5 3fga 9.5 16.8

510 26 6 521.818 4 0.4 0.35 32.51 2 3fga

511 2 1 751.902 4 0.2 0.46 31.05 5 3fga 19 24.6

512 61 4 673.7 6 0.8 0.5 28.78 3 3fga 14.6 16.9

513 9 3 568.817 4 0.8 0.26 36.74 4 3fga 18.4 24.1

514 12 3 1191.974 3 6.2 0.35 26.03 4 3fga

515 1 1 1191.974 3 6.2 0.31 24.18 3 3fga 3.8 3.8

516 5 3 371.98 4 1.5 0.26 35.69 3 3fga 12.3 14.7

517 4 1 710.397 4 3.6 0.62 35.37 4 3fga 9.7 17.7

518 6 1 730.154 4 0.2 0.65 33.88 4 3fga 18.3 22.8

519 3 2 576.03 3 1 0.31 21.6 1 3fga 4.9 5.1

520 7 3 747.176 4 2.2 0.39 31.49 1

521 1 1 573.557 4 -1.3 0.45 34.33 4

86  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

522 8 4 783.676 4 1.1 0.5 30.65 3

523 2 1 588.104 4 4.9 0.53 40.8 7 3fga 17 29.8

524 13 2 589.965 5 3.6 0.42 40.09 8 3fga 12.8 19

525 11 2 600.92 5 2.7 0.45 38.09 6 3fga 14.4 17.9

526 1 1 562.139 5 2.2 0.33 32.24 4 3fga 12.7 13.9

527 10 2 1205.608 4 5.5 0.66 29.71 5 3fga 17.7 20.5

528 2 1 632.602 4 2.9 0.42 28.88 3 3fga 25.5 31.7

529 3 1 615.357 4 4 0.37 26.42 4 3fga 13 15

530 128 5 1129.98 3 6.2 0.69 36.16 8 3fga 13.7 16.3

531 48 5 791.1 3 3.9 0.29 32.76 4 3fga 12.7 18.1

532 31 5 1066.568 4 7 0.48 31.53 4 3fga 18.6 29.2

533 2 1 734.41 4 2.2 0.46 29.81 3 3fga 18.4 23.4

534 26 3 926.502 3 2.3 0.65 39.43 6

535 4 2 603.844 4 -0.3 0.48 38.38 5

536 16 3 472.027 4 2.9 0.5 38.37 4

537 21 2 545.82 4 2 0.53 36.45 4

538 3 2 648.105 4 2.5 0.42 36.24 4

539 5 2 669.688 3 -0.1 0.43 35.33 3

540 103 3 567.308 4 -0.8 0.54 34.32 4

541 3 2 730.879 4 1.8 0.72 32.66 1

542 14 3 648.104 4 2.1 0.43 32.45 4

543 2 2 772.171 4 -2.1 0.38 31.48 2

544 1 1 501.478 5 3.3 0.44 31.34 3

545 2 1 915.493 4 1.1 0.56 31.33 5

546 3 1 587.57 4 1.7 0.48 30.63 3

547 1 1 743.658 4 0.9 0.41 29.85 5

548 2 2 730.879 4 2.3 0.41 28.11 2

549 3 2 612.827 4 0.9 0.33 26.75 3

550 2 1 529.054 4 1.1 0.28 26.52 3

551 2 2 543.305 4 1 0.11 25.82 4

552 11 4 587.57 4 2.1 0.5 38.57 5

553 1 1 400.742 4 1.9 0.54 35.91 3

554 2 2 979.896 3 1.3 0.46 34.8 8

555 3 1 495.022 4 -0.1 0.25 27.74 3

556 1 1 527.047 4 1.6 0.24 25.86 3

557 2 1 590.642 3 0.4 0.14 22 3

558 3 2 781.434 5 5.8 0.55 36.4 7

559 3 1 524.796 6 1.8 0.33 35.15 5

560 1 1 488.53 4 0.4 0.17 26.05 3

561 6 2 674.572 4 2 0.42 32.52 2

562 6 3 425.397 6 0.8 0.19 32.71 3

563 1 1 647.09 4 2.5 0.34 29.13 1

564 3 1 767.211 4 3.9 0.7 24.02 3

565 6 2 852.136 3 5.6 0.48 35.11 6

566 4 1 578.84 4 1.3 0.54 33.68 4

567 9 2 595.838 4 -0.8 0.59 28.12 4

568 3 2 476.872 5 -1 0.13 27.84 3

569 3 1 745.808 5 2.6 0.32 25.43 2

570 7 2 504.623 3 -1.3 0.11 33.87 5 3dw8 12.4 17.6

571 1 1 699.624 4 0.3 0.34 22.19 6

572 10 2 358.813 5 1 0.65 39.96 4

573 17 2 482.517 4 0 0.44 38.97 5

574 34 2 1144.624 3 2.6 0.62 35.92 5

575 1 1 598.344 4 1.1 0.44 33.95 4

576 10 2 646.142 5 4.2 0.42 31.17 4

577 1 1 558.064 4 -0.7 0.3 26.57 3

578 1 1 568.069 4 -1.1 0.09 20.47 1

579 3 2 755.009 5 -0.2 0.37 27.06 3

580 1 1 706.597 4 2.2 0.33 32.4

581 2 1 582.842 4 4.7 0.32 31.61

582 2 1 595.07 4 5 0.29 29.88

583 6 3 665.349 5 5.1 0.53 29.11

584 1 1 652.331 4 -1.4 0.22 29.1

585 1 1 615.079 4 6.5 0.22 26.28

586 2 2 496.602 6 1.7 0.45 25.82

587 1 1 713.119 4 1 0.31 25.8

588 1 1 533.791 4 -2.5 0.3 26.52

589 1 1 634.353 5 0.7 0.36 26.28 2

590 1 1 416.803 7 -0.8 0.3 25.47 3

591 1 1 701.866 4 2.3 0.26 27.17 3

592 2 2 816.43 4 4 0.4 26.57 4

593 10 7 627.356 4 3.9 0.69 41.36 6

594 23 10 756.378 3 1.5 0.44 34.24 5

595 3 2 597.579 4 1.6 0.52 32.13 4

596 2 2 738.683 4 3.6 0.31 23.72 4

597 2 1 717.169 4 2.1 0.37 23.55 1

598 23 10 544.319 5 2.1 0.34 37.4 5

599 2 2 736.859 4 1.7 0.31 35.09 4 2ejm 12.7 19.8

87  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

600 17 4 628.616 4 4.6 0.38 34.12 5

601 2 1 617.087 4 2.2 0.46 29.59 3

602 4 4 678.397 4 3.6 0.14 27.64 5

603 33 11 565.571 4 0.5 0.65 41.93 5

604 154 17 544.319 5 3.3 0.33 40.66 6

605 10 8 871.669 5 -3.6 0.78 34.11 6

606 28 10 819.088 3 5.9 0.51 36.58 6 TRiC 13.7 21.1

607 23 6 897.497 3 5.7 0.54 40.76 5 TRiC 15.7 19.7

608 19 8 957.191 3 0.6 0.45 39.22 7 TRiC 9 10

609 40 8 1013.776 4 4 0.56 36.21 5 TRiC 10.7 16.5

610 13 5 538.899 5 1.5 0.44 33.4 3 TRiC 14 25.4

611 4 2 538.897 5 -1.3 0.41 30.97 3 TRiC 8.7 10.1

612 12 6 811.477 5 6.7 0.26 29.89 7 TRiC 13.9 18.5

613 4 2 726.201 5 2.2 0.79 36.33 6 TRiC 11.6 13.5

614 32 11 528.567 4 0.2 0.59 40.68 5 TRiC 12.8 16.7

615 7 2 582.821 6 2.7 0.44 38.14 6 TRiC 12.4 19.9

616 4 4 423.054 5 -3 0.34 31.3 3 TRiC 20.3 23.6

617 1 1 550.564 4 -3.8 0.48 29.87 3 TRiC 11.1 17.3

618 4 2 436.011 4 -2 0.25 28.35 3 TRiC 13 18.4

619 1 1 891.867 5 -0.1 0.28 21.18 2 TRiC 30 31.2

620 16 5 920.118 5 5.8 0.36 20.09 2 TRiC 14.1 18.5

621 2 1 539.536 4 -1.1 0.45 34.01 2

622 10 5 402.747 4 2.4 0.44 35.41 5

623 1 1 747.152 4 -1.4 0.17 26.05 4

624 15 6 545.561 7 4 0.71 31.4 4

625 23 9 651.025 6 5.2 0.63 30.18 3

626 4 3 1022.296 4 3.8 0.37 28.47 9

627 4 2 1275.178 4 -0.9 0.31 26.32 10

628 1 1 880.869 5 2.5 0.42 21.9 1

629 1 1 890.945 4 3.1 0.3 21.63 4

630 85 12 658.85 4 2.3 0.58 38.48 6

631 18 9 759.804 5 1.7 0.65 36.91 4

632 32 8 573.11 4 4.3 0.75 35.94 1

633 14 6 1171.831 4 1 0.52 33.91 6

634 25 7 520.118 6 3.5 0.41 37.19 3

635 11 2 576.919 5 3.4 0.68 40.61 6

636 6 2 598.74 5 1.5 0.5 38.49 7

637 1 1 695.209 6 4.2 0.5 33.69 3

638 8 2 647.768 5 5.3 0.47 32.01 2

639 1 1 859.671 5 6.9 0.5 27.26 3

640 1 1 716.558 6 3.5 0.57 26.24 2

641 1 1 742.735 3 2 0.1 24.77 3

642 4 2 643.619 4 2.5 0.63 39.09 5

643 3 1 702.721 3 2.5 0.55 38.73 4

644 2 1 645.827 4 1.7 0.55 34.96 5

645 4 2 575.573 4 1.7 0.29 34.12 4

646 2 1 489.453 5 -1.2 0.48 32.37 3

647 82 2 636.114 5 4.3 0.52 39.24 6

648 15 2 604.891 5 -0.4 0.48 37.08 6

649 1 1 684.356 5 3.4 0.43 31.51 4

650 7 2 592.711 5 2.4 0.5 29.95 4

651 2 1 896.057 5 -1 0.55 29.38 2

652 2 2 564.275 5 0.9 0.43 28.21 2

653 6 1 775.433 4 4 0.61 39.94 8

654 10 2 693.851 6 6.6 0.69 38.74 5

655 61 2 775.432 4 3.4 0.6 38.37 7

656 30 2 727.387 5 5.3 0.43 37.89 7

657 1 1 1098.31 4 3.5 0.63 37.64 10

658 5 1 744.158 4 1.1 0.39 37.32 5

659 36 2 691.78 5 4.1 0.47 37.02 5

660 6 2 554.303 4 1.5 0.47 36.79 4

661 30 2 510.114 6 0.9 0.39 36.59 5

662 5 2 729.628 4 0.8 0.59 36.5 4

663 13 2 847.131 3 0.3 0.46 35.86 6

664 2 2 1115.829 4 3.9 0.73 35.14 7

665 4 2 653.617 4 1.4 0.55 34.89 5

666 3 1 506.485 5 0.4 0.52 34.74 4

667 7 2 660.854 4 -1.1 0.36 34.35 4

668 2 2 1145.863 4 5.5 0.61 33.8 7

669 13 2 519.849 7 2.9 0.41 32.98 4

670 15 2 1048.054 4 4.1 0.54 32.43 5

671 9 2 597.077 4 -0.1 0.33 32.37 7

672 7 2 405.836 5 0.4 0.39 31.02 3

673 7 2 571.969 6 1.2 0.41 29.81 2

674 2 2 521.285 5 1.9 0.5 29.32 4

675 2 1 696.624 4 1.6 0.34 28.57 3

676 1 1 880.626 5 0.5 0.39 27.98 4

677 3 3 694.648 7 1.1 0.39 27.6 6

88  

No. N_Id N_Exp m/z z Error [ppm] Tic

Id-Score X ions PDB Euclidean

[Å] SAS [Å]

678 4 2 564.328 4 4.5 0.34 24.43 3

679 2 1 918.882 5 -2.4 0.25 24.1 3

680 1 1 612.348 5 1.6 0.26 23.65 4

681 1 1 971.547 4 2.7 0.55 23.58 7

682 1 1 816.025 5 2 0.22 22.51 1

683 1 1 807.228 5 2.9 0.27 21.68 3

684 5 2 740.411 4 5.5 0.49 38.95 6

685 39 4 722.045 3 2.5 0.41 38.89 5

686 2 2 981.485 4 3.2 0.52 38.02 10

687 12 3 687.572 5 4.2 0.74 37.71 5

688 14 2 606.34 4 2 0.74 36.92 4

689 5 1 580.319 5 1 0.47 36.08 5

690 68 2 651.353 4 0.4 0.35 35.48 5

691 5 2 558.571 4 1.1 0.44 35.18 4

692 4 2 664.117 4 2.6 0.59 34.76 6

693 1 1 765.648 4 2.8 0.43 33.92 6

694 3 2 523.095 5 1.5 0.78 31.86 5

695 4 2 907.14 3 1.3 0.41 31.37 7

696 2 1 700.365 4 -1.2 0.52 31.25 2

697 23 2 588.073 4 0.9 0.42 30.9 0

698 1 1 573.809 4 1 0.34 29.99 1

699 1 1 626.323 4 -0.8 0.32 29.78 3

700 1 1 615.843 4 1.4 0.4 28.33 3

701 1 1 716.4 4 3.1 0.36 27.61 2

702 1 1 1018.3 5 3.4 0.56 27.48 2

703 1 1 519.286 5 -0.1 0.3 27.02 1

704 1 1 750.621 4 1.8 0.35 26.7 3

705 1 1 949.224 4 1.2 0.37 25.36 2

706 2 1 860.061 5 0.2 0.5 25.14 4

707 1 1 1249.143 4 4.9 0.4 25.1 4

708 2 1 1259.645 3 5.3 0.52 24.21 6

709 7 2 647.959 5 6.4 0.73 38.51 3

710 1 1 537.566 4 1 0.45 28.85 4

711 1 1 898.486 3 6.9 0.16 25.21 5

712 2 1 661.877 4 5.2 0.48 25.41 4

713 8 2 428.03 5 -3.5 0.73 38.35 6 3dw8 25.8 28.9

714 9 2 608.128 5 -1.9 0.69 38.06 3 3dw8 27.6 51.5

715 2 2 1010.248 4 4 0.53 33.84 7 3dw8 16.7 22.1

716 20 2 351.214 5 -1.2 0.79 44.4 4 3dw8 22 29

717 9 3 768.42 3 -1.8 0.71 38.88 4 3dw8 20.2 26.9

718 10 3 725.714 3 -1.2 0.52 36.32 5 3dw8 26.4 37.9

719 1 1 838.447 5 2.1 0.46 28.66 3 3dw8 24.2 36.4

720 3 2 904.797 3 0.9 0.53 28.36 3 3dw8 26.6 38.2

721 6 2 591.323 3 -3 0.33 25.87 5 3dw8 30.9 42

722 1 1 636.663 3 -2.2 0.25 25.18 5 3dw8 28.1 38.2

723 3 2 630.023 3 -2.4 0.26 23.39 3 3dw8 17.9 23.2

724 9 2 837.939 4 2.3 0.4 33.95 7

725 16 2 899.202 4 -0.4 0.47 36.97 6

726 3 2 696.769 5 1.8 0.45 28.2 2

727 3 2 591.54 4 1.1 0.32 27.95 3

728 1 1 476.283 4 0.5 0.66 33.83 4

729 25 6 591.539 4 0.1 0.4 33.13 2

730 5 2 591.54 4 1.3 0.36 30.04 3

731 6 3 798.165 4 -0.1 0.38 29.62 4 3c5v 17.2 22.5

89  

Table S6. Target and template information for the generation of comparative protein

models. (No., number)

UniProt entry name (_HUMAN)

Template PDB

entry – Chain ID

Template UniProt

entry name (_HUMAN)

No. of intra-

protein XLs

No. of intra-protein XLs

with coordinates in the model

No. of validated

intra-protein XLs

RMSD [Å]

Sequence identity [%]

2AAB 3FGA-A 2AAA 29 29 13 2.269 83.9 2AAB 3DW8-A 2AAA 29 29 13 3.204 83.5 2A5A 3FGA-B 2A5G 7 6 6 1.535 60.0 2A5D 3FGA-B 2A5G 28 11 11 1.254 59.5 2A5E 3FGA-B 2A5G 11 11 11 1.488 62.8 2ABA 3DW8-B 2ABA 17 17 14 2.014 94.0 2ABD 3DW8-B 2ABA 1 1 1 1.979 83.7 2ABG 3DW8-B 2ABA 18 18 10 2.204 77.7 PP2AB 3FGA-C PP2AA 1 1 1 1.225 95.1 PP2AB 3DW8-C PP2AA 1 1 1 0.830 91.3 PP4C 2IE4-C PP2AA 6 6 6 1.146 63.5

90  

Table S7. Intra-protein cross-link distances of the IGBP1 full length-model IGBP1_1.

Euclidean distances and SAS distances were measured between the Cβ atoms of the lysine

residues using Xwalk. The five cross-links with SAS distances > 34.0 Å (blue background)

were classified as not valid in model IGBP1_1 (chapters M10.2.3 and M10.2.4).

Residue number 1 Residue number 2 Euclidean distance SASD 253 276 8.0 8.0 295 325 7.9 8.8 287 166 11.0 11.0 306 166 10.7 11.2 176 41 11.2 13.1 287 163 13.2 13.6 158 163 9.1 13.9 253 241 11.9 14.0 241 276 10.5 14.5 91 241 13.2 14.5 287 165 13.3 14.5 306 287 9.3 14.6 165 158 10.4 15.1 166 158 12.4 16.4 77 176 14.5 16.6 241 165 16.1 16.7 325 241 12.9 16.9 287 158 12.7 17.0 44 166 17.0 17.0 176 166 14.5 18.9 44 97 14.4 19.1 176 165 16.1 19.8 276 158 12.2 19.9 241 41 18.1 19.9 241 166 19.0 20.4 241 158 16.3 21.6 295 287 12.0 22.2 325 41 16.9 22.5 295 241 10.1 24.0 241 163 21.3 24.1 241 44 23.2 24.2 176 163 19.9 25.2 241 287 17.5 25.9 41 158 22.1 25.9 276 41 22.9 26.2 276 166 18.2 26.3 216 241 20.3 26.5 253 325 24.5 27.1 176 241 26.1 27.9 325 44 21.5 28.0 306 241 24.1 28.4 325 276 22.6 29.0 325 166 22.2 29.5 176 97 22.4 30.1 176 158 26.2 30.5 295 276 17.6 30.9 176 276 27.0 31.2 295 163 21.4 31.5 44 158 27.5 31.5

91  

Residue number 1 Residue number 2 Euclidean distance SASD 325 97 16.9 31.8 253 287 26.2 31.9 295 41 18.9 32.2 325 158 22.8 32.3 295 166 19.3 32.5 253 44 27.9 32.6 241 97 20.6 33.4 306 325 21.1 33.7 253 295 21.7 33.8 306 276 26.7 33.8 287 325 15.7 33.9 325 163 26.2 34.8 97 166 26.5 37.4

295 44 24.6 37.5

306 97 26.6 39

287 97 26.3 44.3

Table S8. Inter-protein cross-link distances of the IGBP1-PP2AA TOP4 model with the

shortest average SAS distances for all inter-protein cross-links.

Distances were measured between Cβ atoms of the lysine residues using Xwalk (TOP4,

chapter M10.2.5)

Residue number 1 Protein 1 Residue number 2 Protein 2 Euclidean distance SASD 35 PP2AA 163 IGBP1 3.8 4.7 33 PP2AA 306 IGBP1 7.0 7.6 28 PP2AA 158 IGBP1 8.0 9.0 40 PP2AA 166 IGBP1 10.6 11.8 33 PP2AA 166 IGBP1 10.5 15.3 40 PP2AA 163 IGBP1 12.7 17.9 40 PP2AA 158 IGBP1 24.0 27.6

Table S9. Inter-protein cross-link distances of the IGBP1-PP4C TOP4 model with the

shortest average SASD for all inter-protein cross-links.

Distances were measured between Cβ atoms of the lysine residues using Xwalk (TOP4,

chapter M10.2.5).

Residue number 1 Protein 1 Residue number 2 Protein 2 Euclidean distance SASD 26 PP4C 166 IGBP1 10.9 13.0 31 PP4C 166 IGBP1 13.1 14.2 31 PP4C 295 IGBP1 20.0 26.1

92  

Table S10. Efficiencies of filters for the selection of protein-protein docking models of

the IGBP1-PP2AA and IGBP1-PP4C complexes.

The filters were applied successively. The maximum Euclidean distance filter was set to

≤30.0 Å, the maximum SAS distance threshold to ≤34.0 Å, intra-protein cross-links and

mono-links had to be solvent-accessible and a minimum binding interface size of ≥900 Å2

was applied (chapters M10.1.3.4 and M10.2.3). The numbers of IGBP1-PP2A and IGBP1-

PP4C models passing the respective filter are listed.

Filter IGBP1-PP2AA

IGBP1- PP4C

0. Total number of generated models 344,910 368,603

1. Number of models after filtering for inter-protein cross-links by Euclidean distance 14,417 10,093

2. Number of models after filtering for inter-protein cross-links by SAS distance 4,154 3,682

3. Number of models after filtering for solvent-accessibility of intra-protein cross-links and mono-links 4,148 3,649

4. Number of models after filtering for binding interfaces ≥ 900 Å2 1,075 1,170

93  

Table S11. Relative and absolute frequencies of predicted interface-residues in IGBP1-

PP2AA and IGBP1-PP4C docking models.

The relative and absolute frequencies of predicted interface-residues for TOP4 models and for

all cluster representatives with the lowest ROSETTA score of the 237 IGBP1-PP2AA and 212

IGBP1-PP4C clusters were calculated (chapters M10.2.3 and M10.2.4). The total numbers of

models for the frequency calculations are shown in brackets. The low interface-frequency of

K158 of IGBP1 may be a result of its position at helix ɑ6 facing the protein center of IGBP

within the model of IGBP1_1 (chapters M10.2.3 and M10.2.4) (fig. S6) (23).

Residue

Relative frequency Absolute frequency

All TOP4 All TOP4 All TOP4 All TOP4 PP2AA PP2AA PP4C PP4C PP2AA PP2AA PP4C PP4C

(237) (37) (212) (36) E37_PP2AA 69% 95% - - 163 35 - - E42_ PP2AA 28% 32% - - 66 12 - -

E34_PP4C - - 65% 81% - - 138 29 R155_IGBP1 47% 43% 63% 53% 111 16 133 19 K158_IGBP1 5% 5% 12% 8% 11 2 25 3 K163_ IGBP1 54% 95% 43% 75% 129 35 91 27

Table S12. Inter-protein cross-link distances between 2ABG and TRiC subunits.

The Euclidean distances were calculated between Cα atoms of lysine residues. The four

selected cross-links to determine the position of 2ABG within the TRiC cavity are highlighted

in blue.

Residue number 1 Protein 1 Residue number 2 Protein 2 Euclidean Distance 383 2ABG 535 TCPE 11.6 389 2ABG 521 TCPH 13.8 260 2ABG 21 TCPG 16 263 2ABG 21 TCPG 20.2 389 2ABG 535 TCPE 21.7 288 2ABG 10 TCPZ 26.9 389 2ABG 530 TCPZ 33.7 389 2ABG 527 TCPB 39.7 389 2ABG 10 TCPZ 41.1 398 2ABG 535 TCPE 42.2 260 2ABG 527 TCPB 44.3 398 2ABG 527 TCPG 46.1 398 2ABG 522 TCPB 51.3 389 2ABG 529 TCPG 56 398 2ABG 21 TCPG 59.9 389 2ABG 29 TCPD 61 389 2ABG 21 TCPG 61.2 383 2ABG 21 TCPG 67.3 389 2ABG 21 TCPD 70.8

94  

Table S13. Estimation of the minimum score threshold for manual validation by a

target-decoy approach.

The affinity-purification of various bait proteins resulted in protein preparations that

significantly differ in protein concentration, complexity and heterogeneity, consequently, the

number and abundances of cross-linked peptides varied to the same extent. Protein samples of

different qualities yielded varying numbers of target hits for intra- and inter-protein cross-

links. The generation of a target-decoy database by reverting the sequence of tryptic peptides

was used to estimate the number of false positive hits. An estimated false positive rate of 0.15

for inter-protein cross-links and 0.10 for intra-protein cross-links was used to determine the

minimum xQuest score threshold for manual validation (-, no cross-link target hits; FPR, false

positive rate; XL, cross-link).

95  

inter‐protein XL  intra‐protein XL 

Bait_replicate  Threshold score  FPR  Threshold score  FPR 

PP4C_1  26  0.08  20  0.07 

PP4C_2  27  0.06  22  0.09 

PP2AA_1  28  0.06  21  0.09 

PP2AA_2  27  0.05  22  0.08 

PP2AB_1  27  0.10  21  0 

PP2AB_2  27  0.08  22  0.05 

PP2AB_3  30  0.13  20  0.04 

PP2AB_4  27  0.13  22  0.06 

PP2AB_5  28  0.14  20  0.02 

2ABA_1  ‐  ‐  26  0 

2ABA_2  22  0  21  0 

2ABG_1  25  0.11  22  0.03 

2ABG _2  23  0  20  0.02 

2ABG _3  25  0.12  21  0.02 

2ABG _4  26  0.13  20  0.02 

2AAB_1  ‐  ‐  20  0.02 

2AAB _2  ‐  ‐  22  0.02 

2A5G_1  28  0.05  21  0.07 

2A5G_2  28  0  20  0.02 

2A5D_1  27  0  21  0 

2A5D_2  21  0  20  0 

2A5E_1  28  0.05  24  0.04 

2A5E_2  28  0.06  24  0.03 

SGOL1_1  29  0.15  24  0.05 

SGOL1_2  30  0.11  24  0.04 

SGOL1_3  30  0.09  24  0.06 

FAM40B_1  ‐  ‐  20  0 

FAM40B_2  ‐  ‐  20  0 

FGFR1OP_1  30  0.15  21  0 

FGFR1OP_2  31  0.15  21  0 

IGBP1_1  26  0.04  20  0.01 

IGBP1_2  27  0.04  21  0.01 

IGBP1_3  27  0.10  20  0.03 

CTTNBP2NL_1  27  0.14  22  0.07 

CTTNBP2NL_2  27  0  23  0.05 

96  

Table S14. Comparison of theoretical and experimental cross-link identifications.

Theoretical cross-links were detected as all lysine pairs that had a SAS distance of ≤ 34.0 Å

between their Cɑ atoms. The structures for the distance calculations were obtained from the

PDB (3FGA, 3DW8) or by comparative modeling (chapters M10.1.3.2 and M10.2.1) (Fig. 4A

and fig. S4).

PP2A TRiC Total

Experimental cross-links 167 176 343

Theoretical cross-links 1089 1530 2619

Percentage 15.3% 11.5% 13.1%

97  

Box S2: Command-line execution command for Euclidean distance calculation with Xwalk. User specific command-line flags are given in curly brackets.

$> java Xwalk -infile {model.pdb} -dist {xls.txt} –mono -euc

{model.pdb}: any PDB file {xls.txt}: text file listing all amino acid pairs that were found to be cross-linked. -mono: switches on the assessment of solvent-accessiblity of mono-link listed in {xls.txt}. -euc: computes only Euclidean distances, skipping SASD calculations.

Box S1: Command-line execution command for Solvent Accessible Surface Distance calculation with Xwalk. User specific command-line flags are given in curly brackets.

$> java Xwalk -infile {model.pdb} -dist {xls.txt} -bb –radius 2.0 –mono {model.pdb}: any PDB file {xls.txt}: text file listing all amino acid pairs that were found to be cross-linked. -bb: excludes all side chain atoms except of C-beta atoms for SASD calculation -radius: probe sphere size for calculating solvent accessibility -mono: switches on the assessment of solvent-accessiblity of mono-link listed in {xls.txt}.

Box S3: Command-line flags for ROSETTA’s loopmodel application. User specific command-line flags are given in curly brackets.

-database {rosetta_DB_dir} -in:file:fullatom -in:file:psipred_ss2 {protein.ss2} -constraints:cst_file {xl.cst} -out:nstruct {n} -loops:input_pdb {model.pdb} -loops:loop_file {loop_file} -loops:frag_sizes 9 3 -loops:frag_files {fragments9} {fragments3} -loops:ccd_closure -loops:remodel quick_ccd -loops:refine refine_ccd -packing:ex1 -packing:ex2 -packing:ex1aro

Supplementary boxes

98  

Box S4: Command-line flags for comparative modelling with ROSETTA. User specific command-line flags are given in curly brackets.

-database {rosetta_DB_dir} -run:protocol threading -run:shuffle -in:file:fasta {protein.fasta} -in:file:psipred_ss2 {protein.ss2} -in:file:template_pdb {template.pdb} -in:file:alignment {protein-template.aln} -out:overwrite -out:nstruct {n} -out:shuffle_nstruct {n} -cm:aln_format general -idealize_after_loop_close -out:file:silent_struct_type binary -loops:extended -loops:build_initial -loops:remodel quick_ccd -loops:relax relax -loops:frag_sizes 9 3 1 -loops:frag_files {fragments9} {fragments3} none -frag9 {fragments9} -frag3 {fragments3} -relax:fast -relax:default_repeats 2 -silent_decoytime -random_grow_loops_by 4 -select_best_loop_from 1 -in:detect_disulf false -fail_on_bad_hbond false -bGDT -evaluation:gdtmm

99  

Box S5: Command-line flags for ROSETTA’s nonlocal application. User specific command-line flags are given in curly brackets.

-database {rosetta_DB_dir} -in:file:fasta {protein.fasta} -in:file:psipred_ss2 {protein.ss2} -in:file:template_pdb {template.pdb} -in:file:alignment {protein-template.aln} -out:overwrite -out:nstruct {n} -cm:aln_format general -frag3 {fragments3} -frag9 {fragments9} -abinitio::relax -abinitio::no_write_failures -abinitio:increase_cycles 1 -abinitio:rg_reweight 0.25 -nonlocal:builder star -nonlocal:mode semirigid -nonlocal:gap_sampling_extension 5 -jumps:ramp_chainbreaks -jumps:overlap_chainbreak -jumps:increase_chainbreak 0.5 -constraints:cst_fa_file {template.cst} -constraints:cst_file {template.cst} -bGDT -evaluation:gdtmm

Box S6: Command-line flags for ROSETTA’s docking_protocol application in low resolution mode. User specific command-line flags are given in curly brackets.

-database {rosetta_DB_dir} -in:file:s {proteins.pdb} -constraints:cst_file {inter-xl.cst} -out:overwrite -out:nstruct {n} -out:file:o {model.pdb} -docking:low_res_protocol_only -docking:randomize1 -docking:randomize2 -docking:spin -docking:docking_centroid_outer_cycles 10 -docking:docking_centroid_inner_cycles 50 -docking:dock_lowres_filter 10 1

100  

Box S7: Command-line flags for ROSETTA’s docking_protocol application for refining the docking position in high-resolution. User specific command-line flag are given in curly brackets.

-database {rosetta_DB_dir} -in:file:s {proteins.pdb} -out:overwrite -out:file:fullatom -docking:docking_local_refine -packing:use_input_sc -docking:dock_rtmin -docking:sc_min -docking:dock_min -packing:ex1 -packing:ex2aro

Box S8: Command-line execution command for generating ROSETTA fragment files. User specific command-line flags are given in curly brackets.

$> make_fragment.pl -nosam -nojufo -noprof -id {id} {protein.fasta}

Box S9: Command-line flags for ROSETTA’s relax application. User specific command-line flag is given in curly brackets.

-database {rosetta_DB_dir} -relax:sequence -constrain_relax_to_start_coords

101

References

1. F. Alber et al., The molecular architecture of the nuclear pore complex. Nature 450, 695

(2007). doi:10.1038/nature06405 Medline

2. P. Aloy, R. B. Russell, Structural systems biology: Modelling protein interactions. Nat. Rev.

Mol. Cell Biol. 7, 188 (2006). doi:10.1038/nrm1859 Medline

3. A. Leitner et al., Probing native protein structures by chemical cross-linking, mass

spectrometry, and bioinformatics. Mol. Cell. Proteomics 9, 1634 (2010).

doi:10.1074/mcp.R000001-MCP201 Medline

4. H. Zhang et al., Identification of protein-protein interactions and topologies in living cells with

chemical cross-linking and mass spectrometry. Mol. Cell. Proteomics 8, 409 (2009).

doi:10.1074/mcp.M800232-MCP200 Medline

5. Z. A. Chen et al., Architecture of the RNA polymerase II-TFIIF complex revealed by cross-

linking and mass spectrometry. EMBO J. 29, 717 (2010). doi:10.1038/emboj.2009.401

Medline

6. S. Jennebach, F. Herzog, R. Aebersold, P. Cramer, Crosslinking-MS analysis reveals RNA

polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Res. 40,

5591 (2012). doi:10.1093/nar/gks220 Medline

7. K. Lasker et al., Molecular architecture of the 26S proteasome holocomplex determined by an

integrative approach. Proc. Natl. Acad. Sci. U.S.A. 109, 1380 (2012).

doi:10.1073/pnas.1120559109 Medline

8. M. A. Lauber, J. P. Reilly, Novel amidinating cross-linker for facilitating analyses of protein

structures and interactions. Anal. Chem. 82, 7736 (2010). doi:10.1021/ac101586z

Medline

9. V. Janssens, J. Goris, Protein phosphatase 2A: A highly regulated family of serine/threonine

phosphatases implicated in cell growth and signalling. Biochem. J. 353, 417 (2001).

doi:10.1042/0264-6021:3530417 Medline

10. G. B. Moorhead, L. Trinkle-Mulcahy, A. Ulke-Lemée, Emerging roles of nuclear protein

phosphatases. Nat. Rev. Mol. Cell Biol. 8, 234 (2007). doi:10.1038/nrm2126 Medline

11. Y. Shi, Serine/threonine phosphatases: Mechanism through structure. Cell 139, 468 (2009).

doi:10.1016/j.cell.2009.10.006 Medline

12. C. Wurzenberger, D. W. Gerlich, Phosphatases: Providing safe passage through mitotic exit.

Nat. Rev. Mol. Cell Biol. 12, 469 (2011). doi:10.1038/nrm3149 Medline

13. D. M. Virshup, S. Shenolikar, From promiscuity to precision: Protein phosphatases get a

makeover. Mol. Cell 33, 537 (2009). doi:10.1016/j.molcel.2009.02.015 Medline

14. M. Goudreault et al., A PP2A phosphatase high density interaction network identifies a novel

striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous

malformation 3 (CCM3) protein. Mol. Cell. Proteomics 8, 157 (2009).

doi:10.1074/mcp.M800266-MCP200 Medline

15. J. R. Hutchins et al., Systematic analysis of human protein complexes identifies chromosome

segregation proteins. Science 328, 593 (2010). doi:10.1126/science.1181348 Medline

102

16. Materials and methods are available as supplementary materials on Science Online.

17. A. Leitner et al., Expanding the chemical cross-linking toolbox by the use of multiple

proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11,

M111.014126 (2012). doi:10.1074/mcp.M111.014126

18. O. Rinner et al., Identification of cross-linked peptides from large sequence databases. Nat.

Methods 5, 315 (2008). doi:10.1038/nmeth0808-748a Medline

19. A. Wepf, T. Glatter, A. Schmidt, R. Aebersold, M. Gstaiger, Quantitative interaction

proteomics using mass spectrometry. Nat. Methods 6, 203 (2009).

doi:10.1038/nmeth.1302 Medline

20. Y. Xu et al., Structure of the protein phosphatase 2A holoenzyme. Cell 127, 1239 (2006).

doi:10.1016/j.cell.2006.11.033 Medline

21. M. Kong, D. Ditsworth, T. Lindsten, C. B. Thompson, Alpha4 is an essential regulator of

PP2A phosphatase activity. Mol. Cell 36, 51 (2009). doi:10.1016/j.molcel.2009.09.025

Medline

22. T. D. Prickett, D. L. Brautigan, Overlapping binding sites in protein phosphatase 2A for

association with regulatory A and alpha-4 (mTap42) subunits. J. Biol. Chem. 279, 38912

(2004). doi:10.1074/jbc.M401444200 Medline

23. M. LeNoue-Newton et al., The E3 ubiquitin ligase- and protein phosphatase 2A (PP2A)-

binding domains of the Alpha4 protein are both required for Alpha4 to inhibit PP2A

degradation. J. Biol. Chem. 286, 17665 (2011). doi:10.1074/jbc.M111.222414 Medline

24. H. Wang, X. Wang, Y. Jiang, Interaction with Tap42 is required for the essential function of

Sit4 and type 2A phosphatases. Mol. Biol. Cell 14, 4342 (2003). doi:10.1091/mbc.E03-

02-0072 Medline

25. P. Bradley, D. Baker, Improved beta-protein structure prediction by multilevel optimization

of nonlocal strand pairings and local backbone conformation. Proteins 65, 922 (2006).

doi:10.1002/prot.21133 Medline

26. J. J. Gray et al., Protein-protein docking with simultaneous optimization of rigid-body

displacement and side-chain conformations. J. Mol. Biol. 331, 281 (2003).

doi:10.1016/S0022-2836(03)00670-3 Medline

27. X. Yan, R. Habedanck, E. A. Nigg, A complex of two centrosomal proteins, CAP350 and

FOP, cooperates with EB1 in microtubule anchoring. Mol. Biol. Cell 17, 634 (2006).

doi:10.1091/mbc.E05-08-0810 Medline

28. T. S. Kitajima et al., Shugoshin collaborates with protein phosphatase 2A to protect cohesin.

Nature 441, 46 (2006). doi:10.1038/nature04663 Medline

29. C. G. Riedel et al., Protein phosphatase 2A protects centromeric sister chromatid cohesion

during meiosis I. Nature 441, 53 (2006). doi:10.1038/nature04664 Medline

30. Z. Xu et al., Structure and function of the PP2A-shugoshin interaction. Mol. Cell 35, 426

(2009). doi:10.1016/j.molcel.2009.06.031 Medline

103

31. S. Muto et al., Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone

chaperone activity. Proc. Natl. Acad. Sci. U.S.A. 104, 4285 (2007).

doi:10.1073/pnas.0603762104 Medline

32. Y. Cong et al., Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-

driven conformational cycle. EMBO J. 31, 720 (2012). doi:10.1038/emboj.2011.366

33. N. Kalisman, C. M. Adams, M. Levitt, Subunit order of eukaryotic TRiC/CCT chaperonin by

cross-linking, mass spectrometry, and combinatorial homology modeling. Proc. Natl.

Acad. Sci. U.S.A. 109, 2884 (2012). doi:10.1073/pnas.1119472109 Medline

34. A. Leitner et al., The molecular architecture of the eukaryotic chaperonin TRiC/CCT.

Structure 20, 814 (2012). doi:10.1016/j.str.2012.03.007 Medline

35. I. G. Muñoz et al., Crystal structure of the open conformation of the mammalian chaperonin

CCT in complex with tubulin. Nat. Struct. Mol. Biol. 18, 14 (2011).

doi:10.1038/nsmb.1971 Medline

36. L. Chen, P. B. Sigler, The crystal structure of a GroEL/peptide complex: Plasticity as a basis

for substrate diversity. Cell 99, 757 (1999). doi:10.1016/S0092-8674(00)81673-6

Medline

37. D. K. Clare et al., ATP-triggered conformational changes delineate substrate-binding and -

folding mechanics of the GroEL chaperonin. Cell 149, 113 (2012).

doi:10.1016/j.cell.2012.02.047 Medline

38. F. Alber et al., Determining the architectures of macromolecular assemblies. Nature 450, 683

(2007). doi:10.1038/nature06404 Medline

39. T. Glatter, A. Wepf, R. Aebersold, M. Gstaiger, An integrated workflow for charting the

human interaction proteome: Insights into the PP2A system. Mol. Syst. Biol. 5, 237

(2009). doi:10.1038/msb.2008.75 Medline

40. F. Herzog, J. M. Peters, Large-scale purification of the vertebrate anaphase-promoting

complex/cyclosome. Methods Enzymol. 398, 175 (2005). doi:10.1016/S0076-

6879(05)98016-6 Medline

41. P. G. Pedrioli et al., A common open representation of mass spectrometry data and its

application to proteomics research. Nat. Biotechnol. 22, 1459 (2004).

doi:10.1038/nbt1031 Medline

42. D. Kessner, M. Chambers, R. Burke, D. Agus, P. Mallick, ProteoWizard: Open source

software for rapid proteomics tools development. Bioinformatics 24, 2534 (2008).

doi:10.1093/bioinformatics/btn323 Medline

43. R. Craig, R. C. Beavis, TANDEM: Matching proteins with tandem mass spectra.

Bioinformatics 20, 1466 (2004). doi:10.1093/bioinformatics/bth092 Medline

44. A. Keller, A. I. Nesvizhskii, E. Kolker, R. Aebersold, Empirical statistical model to estimate

the accuracy of peptide identifications made by MS/MS and database search. Anal.

Chem. 74, 5383 (2002). doi:10.1021/ac025747h Medline

104

45. A. I. Nesvizhskii, A. Keller, E. Kolker, R. Aebersold, A statistical model for identifying

proteins by tandem mass spectrometry. Anal. Chem. 75, 4646 (2003).

doi:10.1021/ac0341261 Medline

46. D. R. Müller et al., Isotope-tagged cross-linking reagents: A new tool in mass spectrometric

protein interaction analysis. Anal. Chem. 73, 1927 (2001). doi:10.1021/ac001379a

Medline

47. J. Seebacher et al., Protein cross-linking analysis using mass spectrometry, isotope-coded

cross-linkers, and integrated computational data processing. J. Proteome Res. 5, 2270

(2006). doi:10.1021/pr060154z Medline

48. M. Ohi, Y. Li, Y. Cheng, T. Walz, Negative staining and image classification: Powerful

tools in modern electron microscopy. Biol. Proced. Online 6, 23 (2004).

doi:10.1251/bpo70 Medline

49. S. J. Ludtke, P. R. Baldwin, W. Chiu, EMAN: Semiautomated software for high-resolution

single-particle reconstructions. J. Struct. Biol. 128, 82 (1999).

doi:10.1006/jsbi.1999.4174 Medline

50. M. van Heel, G. Harauz, E. V. Orlova, R. Schmidt, M. Schatz, A new generation of the

IMAGIC image processing system. J. Struct. Biol. 116, 17 (1996).

doi:10.1006/jsbi.1996.0004 Medline

51. D. N. Mastronarde, Automated electron microscope tomography using robust prediction of

specimen movements. J. Struct. Biol. 152, 36 (2005). doi:10.1016/j.jsb.2005.07.007

Medline

52. J. A. Mindell, N. Grigorieff, Accurate determination of local defocus and specimen tilt in

electron microscopy. J. Struct. Biol. 142, 334 (2003). doi:10.1016/S1047-

8477(03)00069-8 Medline

53. P. Dube, P. Tavares, R. Lurz, M. van Heel, The portal protein of bacteriophage SPP1: A

DNA pump with 13-fold symmetry. EMBO J. 12, 1303 (1993). Medline

54. M. van Heel, J. Frank, Use of multivariate statistics in analysing the images of biological

macromolecules. Ultramicroscopy 6, 187 (1981). Medline

55. M. Van Heel, Angular reconstitution: A posteriori assignment of projection directions for 3D

reconstruction. Ultramicroscopy 21, 111 (1987). doi:10.1016/0304-3991(87)90078-7

Medline

56. D. K. Clare et al., Multiple states of a nucleotide-bound group 2 chaperonin. Structure 16,

528 (2008). doi:10.1016/j.str.2008.01.016 Medline

57. C. V. Robinson, A. Sali, W. Baumeister, The molecular sociology of the cell. Nature 450,

973 (2007). doi:10.1038/nature06523 Medline

58. D. Mourado, B. Kobe, N. E. Dixon, T. Huber, in Introduction to Protein Structure

Prediction, H. Rangwala, G. Karypis, Eds. (Wiley, Hoboken, NJ, USA, 2010), pp. 265–

277.

105

59. F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali, Integrating diverse data for structure

determination of macromolecular assemblies. Annu. Rev. Biochem. 77, 443 (2008).

doi:10.1146/annurev.biochem.77.060407.135530 Medline

60. H. M. Berman et al., The Protein Data Bank. Nucleic Acids Res. 28, 235 (2000).

doi:10.1093/nar/28.1.235 Medline

61. R. Das, D. Baker, Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 77, 363

(2008). doi:10.1146/annurev.biochem.77.062906.171838 Medline

62. K. W. Kaufmann, G. H. Lemmon, S. L. Deluca, J. H. Sheehan, J. Meiler, Practically useful:

What the Rosetta protein modeling suite can do for you. Biochemistry 49, 2987 (2010).

doi:10.1021/bi902153g Medline

63. A. Kahraman, L. Malmström, R. Aebersold, Xwalk: Computing and visualizing distances in

cross-linking experiments. Bioinformatics 27, 2163 (2011).

doi:10.1093/bioinformatics/btr348 Medline

64. A. Zelter et al., Isotope signatures allow identification of chemically cross-linked peptides by

mass spectrometry: A novel method to determine interresidue distances in protein

structures through cross-linking. J. Proteome Res. 9, 3583 (2010).

doi:10.1021/pr1001115 Medline

65. D. Baker, Prediction and design of macromolecular structures and interactions. Philos. Trans.

R. Soc. Lond. B Biol. Sci. 361, 459 (2006). doi:10.1098/rstb.2005.1803 Medline

66. C. A. Rohl, C. E. Strauss, K. M. Misura, D. Baker, Protein structure prediction using Rosetta.

Methods Enzymol. 383, 66 (2004). doi:10.1016/S0076-6879(04)83004-0 Medline

67. D. E. Kim, D. Chivian, D. Baker, Protein structure prediction and analysis using the Robetta

server. Nucleic Acids Res. 32, (Web Server issue), W526 (2004). doi:10.1093/nar/gkh468

Medline

68. D. T. Jones, Protein secondary structure prediction based on position-specific scoring

matrices. J. Mol. Biol. 292, 195 (1999). doi:10.1006/jmbi.1999.3091 Medline

69. P. Rice, I. Longden, A. Bleasby, EMBOSS: The European Molecular Biology Open Software

Suite. Trends Genet. 16, 276 (2000). doi:10.1016/S0168-9525(00)02024-2 Medline

70. C. Wang, P. Bradley, D. Baker, Protein-protein docking with backbone flexibility. J. Mol.

Biol. 373, 503 (2007). doi:10.1016/j.jmb.2007.07.050 Medline

71. A. A. Canutescu, R. L. Dunbrack, Jr., Cyclic coordinate descent: A robotics algorithm for

protein loop closure. Protein Sci. 12, 963 (2003). doi:10.1110/ps.0242703 Medline

72. A. Kahraman, R. J. Morris, R. A. Laskowski, A. D. Favia, J. M. Thornton, On the diversity

of physicochemical environments experienced by identical ligands in binding pockets of

unrelated proteins. Proteins 78, 1120 (2010). doi:10.1002/prot.22633 Medline

73. A. Kahraman, R. J. Morris, R. A. Laskowski, J. M. Thornton, Shape variation in protein

binding pockets and their ligands. J. Mol. Biol. 368, 283 (2007).

doi:10.1016/j.jmb.2007.01.086 Medline

74. J. Thompson, D. Baker, Incorporation of evolutionary information into Rosetta comparative

modeling. Proteins 79, 2380 (2011). doi:10.1002/prot.23046 Medline

106

75. S. Hubbard, J. Thornton, Naccess (Computer Program, Department of Biochemistry and

Molecular Biology, University College London, 1993).

76. S. Bohn et al., Structure of the 26S proteasome from Schizosaccharomyces pombe at

subnanometer resolution. Proc. Natl. Acad. Sci. U.S.A. 107, 20992 (2010).

doi:10.1073/pnas.1015530107 Medline

77. R. Apweiler et al., UniProt: The Universal Protein knowledgebase. Nucleic Acids Res. 32,

115 (2004). doi:10.1093/nar/gkh131

78. C. Chothia, A. M. Lesk, The relation between the divergence of sequence and structure in

proteins. EMBO J. 5, 823 (1986). Medline

79. D. Korkin et al., Structural modeling of protein interactions by analogy: Application to PSD-

95. PLOS Comput. Biol. 2, e153 (2006). doi:10.1371/journal.pcbi.0020153 Medline

80. G. Kleywegt, T. Jones, CCP4/ESF-EACBM Newsletter on Protein Crystallography, 9 (30

November 1994).

81. J. Söding, A. Biegert, A. N. Lupas, The HHpred interactive server for protein homology

detection and structure prediction. Nucleic Acids Res. 33, (Web Server issue), W244

(2005). doi:10.1093/nar/gki408 Medline

82. H. Hwang, T. Vreven, B. G. Pierce, J. H. Hung, Z. Weng, Performance of ZDOCK and

ZRANK in CAPRI rounds 13-19. Proteins 78, 3104 (2010). doi:10.1002/prot.22764

Medline

83. A. Sali, T. L. Blundell, Comparative protein modelling by satisfaction of spatial restraints. J.

Mol. Biol. 234, 779 (1993). doi:10.1006/jmbi.1993.1626 Medline

84. J. Yang, S. M. Roe, T. D. Prickett, D. L. Brautigan, D. Barford, The structure of

Tap42/alpha4 reveals a tetratricopeptide repeat-like fold and provides insights into PP2A

regulation. Biochemistry 46, 8807 (2007). doi:10.1021/bi7007118 Medline

85. M. Bantscheff, M. Schirle, G. Sweetman, J. Rick, B. Kuster, Quantitative mass spectrometry

in proteomics: A critical review. Anal. Bioanal. Chem. 389, 1017 (2007).

doi:10.1007/s00216-007-1486-6 Medline

86. O. Llorca et al., Eukaryotic type II chaperonin CCT interacts with actin through specific

subunits. Nature 402, 693 (1999). doi:10.1038/45294 Medline