Snf5 and Swi3 subcomplex formation is required for SWI/SNF complex function in yeast Hao Zhou a, *, 1 , Guidong Chen a, 1 , Chunming Dong b, 1 , Xiaozhou Zhao a , Zhongtian Shen a , Feilong Chen a , Beibei liu a , and Jiafu Long a, ** a State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China b State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China * Corresponding author. ** Corresponding author. E-mail addresses: [email protected](H, Zhou), [email protected](J, Long) 1 These three authors contributed equally to this work. Keywords: Chromatin remodeling complex, SWI/SNF complex, BAF complex, Snf5-Swi3 subcomplex Running title: Crystal structure of the Snf5-Swi3 subcomplex
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Snf5 and Swi3 subcomplex formation is required for SWI/SNF ...€¦ · Snf5 and Swi3 subcomplex formation is required for SWI/SNF complex function in yeast Hao Zhoua, *, 1, Guidong
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Snf5 and Swi3 subcomplex formation is required for
Snf5_S.c E LVPIRL LRD N N E D ED T E D D W DKLI F D M A KLKVYKQAMNE S Q F QDR RFF TLL K KI D V D LR YRFED TREQHSnf5_C.e E LVPIRL LRD N N E D D NA DMEL DG K FTF EKMITP EIMCE LDL A F LEMSKRVMK EEG D .. I T K MIA PL V... SMARCB1_D.m E LVPIRL LRD N N E D DD NA Q DMEL EG K FTW E MITP F EVLCD LDL L F TDPTASLE A K C .. Q T K S Q A NP P... SMARCB1_D.r E LVPIRL LRD N N E D DD NA Q DMEI DG K FTW EKLMTP F EILCD LDL L F HDPAVIHE S Q V .. Q A M M A SP T... SMARCB1_M.m E LVPIRL LRD N N E D DD NA Q DMEI DG K FTW EKLMTP F EILCD LDL L F HDPAVIHE S P V .. Q A M M S NP T... SMARCB1_H.s E LVPIRL LRD N N E D DD NA Q DMEI DG K FTW EKLMTP F EILCD LDL L F HDPAVIHE S P V .. Q A M M S NP T...
Snf5_S.c I I Q D R KL I VG L DQ EWD S N PE F I Q I F I I I Q Q I F I A M DT C S QE QE QGNPY ELNQDRLGGD L R D V N NSD C E ES Snf5_C.e I I Q D R KL I VG L DQ EWD S N PE F PA A Q LE L Q AVL N N S V F M D S IQ TA N ASTEAPP DVN.....IC N Q PN E SRN SMARCB1_D.m I I Q D R KL I VG L DQ EWD S N PE F VPA QA Q IE F I Q VIV N N S V M E N A L A R A PNDPP LEE.....TC H T V KN E IK SMARCB1_D.r I I Q D R KL I VG L DQ EWD S N PE F VPA SA Q IE Y I Q VII N N S V F M E S A L A R S PTDS. LDE.....QM H I KE K LK SMARCB1_M.m I I Q D R KL I VG L DQ EWD S N PE F VPA SA Q IE Y I Q VII N N S V F M E S A L A R S PTDS. LED.....QS H I KE K LK SMARCB1_H.s I I Q D R KL I VG L DQ EWD S N PE F VPA SA Q IE Y I Q VII N N S V F M E S A L A R S PTDS. LED.....QS H I KE K LK
Snf5_S.c C EL L GEF IA SIR Q A F P T R P VT V KS S LD E F Q E A H E HMYH L LLGYN DG AIEDDDIRSRML TI DVY PAA SKI TSnf5_C.e C EL L GEF IA SIR Q A F P T R G G MS Y G LQW RTY SES L VD T EVE W K G NQ ..... ............ A CPF SS S GSMARCB1_D.m C EL L GEF IA SIR Q A F P T R G G VT Y G LSW RTY SE L ID N DAD W A A HC ..... A............ S VPF PS A ASMARCB1_D.r C EL L GEF IA SIR Q A F P T R G G VT Y G LSW RTY SEN L VE N DAD W S T HQ ..... ............ P IAI TG Q CSMARCB1_M.m C EL L GEF IA SIR Q A F P T R G G VT Y G LSW KTY SEN L VE N DAD W S T HQ ..... ............ P IAI TG Q CSMARCB1_H.s C EL L GEF IA SIR Q A F P T R G G VT Y G LSW KTY SEN L VE N DAD W S T HQ ..... ............ P IAI TG Q C
Snf5_S.c P L AE E D DR TRR RR QIS L R K S N L A LD K D K QGR NRRG P18480Snf5_C.e P L AE E D DR TRR RR ETLTD I KKMR Q N M LV Y F GGGFN Q21831SMARCB1_D.m P L AE E D DR TRR RR ETLTD M KKIR Q N M LA T W F N TTG Q24090SMARCB1_D.r P L AE E D DR TRR RR ETLTD M KKIR Q N M LA T W L N APA Q5U39SMARCB1_M.m P L AE E D DR TRR RR ETLTD M KKIR Q N M LA T W SMARCB1_H.s P L AE E D DR TRR RR ETLTD M KKIR Q N M LA T W L N APA Q12824
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Rpt1-β1 Rpt1-β2 Rpt1-α1 Rpt1-α2
Rpt1-α2 Rpt2-β3 Rpt2-β4 Rpt2-α4Rpt2-α3
Rpt2-α5 Rpt2-α6Rpt2-α7
Rpt2-α8
L N APA Q9Z0H3
Rpt2-β5α9 667
Supplementary Figure S1
Snf5(454-680)
Snf5(454-680)
Snf5(454-680)
Snf5(454-680)
* * *
**
Supplementary Figure S1. Structure-based sequence alignment of Snf5 from different species. Multiple sequence alignment of Snf5 or SMARCB1. The conserved residues are shaded red, and the secondary structure of Snf5 according to the crystal structure of Snf5(454-680)/Swi3(212-398) is shown at the top. Constructs in which highly conserved residues in Snf5 were mutated (Snf5(D475A, D483A, D498A), Snf5(T591A), Snf5(D475A, D483A, D498A, T591A)/Snf5(Rpt1*), Snf5(E582A)/Snf5(Rpt2*), or Snf5(D475A, D483A, D498A, E582A, T591A)/Snf5(Rpt1*, Rpt2*)) are indicated with black asterisks. Species abbreviations: H.s, Homo sapiens; M.m, Mus musculus; D.r, Danio rerio; D.m, Drosophila melanogaster; C.e, Caenorhabditis elegans; S.c, Saccharomyces cerevisiae. The GenBank numbers are shown at the end of the alignment.
Swi3_S.c S T S E G ES L A P IP A A I D V G E QE E M DN IF DTKS KQ GN SSV NT E D HK EQEDI EKTESV .KK DS ..E RN R I NDHSwi3_C.e S T S E KR RDDD DV D DD G A V VPK KD E KG LTDLD GA .R DG SM .G D . RS A VK E ..GKE A FSAP QK EGV......SMARCC2_D.r S T S E KRG REEEQ DL ELDEP VP V A LPK V KD D VKGG MTDLD QE E M TK Q E .. .K P A EE T T T.K S STP T D S ETVSMARCC2_M.m S T S E KRG REEEQ DL DMDEP VP V V LPK V KD E VKGG MTDLD QD E M TK H E .. .K P N EE T T NTK S SAP T D S ETTSMARCC2_H.s S T S E KRG REEEQ DL DMDEP VP V V LPK V KD E VKGG MTDLD QE E M TK H E .. .K P N EE T T NTK S SAP T D S ETT
Swi3_S.c E Q H I PSY WF H IE PEFF SKTP K T VI I L T R EVS SAN......PKK TITRVEP TFEIP A E SK NLEK S VQS N IP Swi3_C.e E Q H I PSY WF H IE PEFF SKTP T L NV E T VV A DYN I KRAM NGKNK DV............QS KEAPQ A G I Y G A Q SMARCC2_D.r E Q H I PSY WF H IE PEFF SKTP K L NV E T II A DYN V RRAL NGKNK EIG EEEEGSPSVKGEPVKGSD H D T H A S A SMARCC2_M.m E Q H I PSY WF H IE PEFF SKTP K Q L NV E T II A DYN V RRAL NGKNK EIG DEDENSTGNKGE TKNPD H D T H A S A SMARCC2_H.s E Q H I PSY WF H IE PEFF SKTP K Q L NV E T II A DYN V RRAL NGKNK EIG DEDENSTGNKGE TKNPD H D T H A S A
Swi3_S.c Y YRNFM YRLNP EY T RRN GD R H FL WGL NYQVD
M V S N S V A AL L I
R N F V TA S A F K TK SKL
Swi3_C.e Y YRNFM YRLNP EY T RRN GD R H FL WGL NYQVD
VA VDT VS AC LA VC IV L EQ L D
F A S S S A
SMARCC2_D.r Y YRNFM YRLNP EY T RRN GD R H FL WGL NYQVD
LA IDT Q LT AC LA VCAIM V EQ I E
S A S S
SMARCC2_M.m Y YRNFM YRLNP EY T RRN GD R H FL WGL NYQVD
LA IDT Q LT AC LA VCAIM V EQ I E
S A A S
SMARCC2_H.s Y YRNFM YRLNP EY T RRN GD R H FL WGL NYQVD
LA IDT Q LT AC LA VCAIM V EQ I E
S A A S
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αA αB
αC αD αE
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P32591 G5EF87 E7FFZ4 Q6PDG5 Q8TAQ2
Supplementary Figure S2Swi3(212-398)
Swi3(212-398)
Swi3(212-398)
* **
Supplementary Figure S2. Structure-based sequence alignment of Swi3 from different species.Multiple sequence alignment of Swi3 or SMARCC2. The conserved residues are shaded red, and thesecondary structure of Swi3 according to the crystal structure of Snf5(454-680)/Swi3(212-398) is shown at the top. Residues R368, R380, and A376, which were mutated in the Swi3(R368A, R380A) or Swi3(A376E) constructs, are indicated with black asterisks. Species abbreviations: H.s, Homo sapiens; M.m, Mus musculus; D.r, Danio rerio; C.e, Caenorhabditis elegans; S.c, Saccharomyces cerevisiae. The GenBank numbers are shown at the end of the alignment.