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- EMDB-20933: SWI/SNF Body Module -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-20933
TitleSWI/SNF Body Module
Map datacryo-EM structure of the yeast SWI/SNF body module
Sample
  • Complex: SWI/SNF Body module
    • Protein or peptide: x 11 types
KeywordsSWI/SNF / chromatin remodeler / TRANSCRIPTION
Function / homology
Function and homology information


carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity ...carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity / nucleosomal DNA binding / nuclear chromosome / positive regulation of transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / maturation of LSU-rRNA / helicase activity / nucleotide-excision repair / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / DNA-templated DNA replication / double-strand break repair / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex ...SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / Helicase/SANT-associated domain / HSA domain profile. / AT hook, DNA-binding motif / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / : / SANT domain profile. / SWIB/MDM2 domain superfamily / SANT domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / Transcription regulatory protein SNF2 / SWI/SNF complex subunit SWI3 / Transcription regulatory protein SNF12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHe Y / Han Y
Funding support United States, 3 items
OrganizationGrant numberCountry
American Cancer SocietyIRG-15-173-21 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA193419 United States
CitationJournal: Nature / Year: 2020
Title: Cryo-EM structure of SWI/SNF complex bound to a nucleosome.
Authors: Yan Han / Alexis A Reyes / Sara Malik / Yuan He /
Abstract: The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel ...The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation.
History
DepositionNov 8, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseMar 18, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6uxv
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20933.png

Downloads & links

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Map

FileDownload / File: emd_20933.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM structure of the yeast SWI/SNF body module
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.039968584 - 0.09254151
Average (Standard dev.)0.00022450463 (±0.0025285592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 430.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0400.0930.000

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Supplemental data

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Sample components

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Entire : SWI/SNF Body module

EntireName: SWI/SNF Body module
Components
  • Complex: SWI/SNF Body module
    • Protein or peptide: Transcription regulatory protein SNF2
    • Protein or peptide: SWI/SNF chromatin-remodeling complex subunit SWI1
    • Protein or peptide: SWI/SNF chromatin-remodeling complex subunit SNF5
    • Protein or peptide: SWI/SNF complex subunit SWI3
    • Protein or peptide: Transcription regulatory protein SNF12
    • Protein or peptide: Transcription regulatory protein SNF6
    • Protein or peptide: Unknown protein
    • Protein or peptide: Unknown protein
    • Protein or peptide: Unknown protein
    • Protein or peptide: SWI/SNF global transcription activator complex subunit SWP82
    • Protein or peptide: Unknown protein

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Supramolecule #1: SWI/SNF Body module

SupramoleculeName: SWI/SNF Body module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Macromolecule #1: Transcription regulatory protein SNF2

MacromoleculeName: Transcription regulatory protein SNF2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 194.315094 KDa
SequenceString: MNIPQRQFSN EEVNRCYLRW QHLRNEHGMN APSVPEFIYL TKVLQFAAKQ RQELQMQRQQ QGISGSQQNI VPNSSDQAEL PNNASSHIS ASASPHLAPN MQLNGNETFS TSAHQSPIMQ TQMPLNSNGG NNMLPQRQSS VGSLNATNFS PTPANNGENA A EKPDNSNH ...String:
MNIPQRQFSN EEVNRCYLRW QHLRNEHGMN APSVPEFIYL TKVLQFAAKQ RQELQMQRQQ QGISGSQQNI VPNSSDQAEL PNNASSHIS ASASPHLAPN MQLNGNETFS TSAHQSPIMQ TQMPLNSNGG NNMLPQRQSS VGSLNATNFS PTPANNGENA A EKPDNSNH NNLNLNNSEL QPQNRSLQEH NIQDSNVMPG SQINSPMPQQ AQMQQAQFQA QQAQQAQQAQ QAQQAQARLQ QG RRLPMTM FTAEQSELLK AQITSLKCLV NRKPIPFEFQ AVIQKSINHP PDFKRMLLSL SEFARRRQPT DQNNQSNLNG GNN TQQPGT NSHYNNTNTD NVSGLTRNAP LDSKDENFAS VSPAGPSSVH NAKNGTLDKN SQTVSGTPIT QTESKKEENE TISN VAKTA PNSNKTHTEQ NNPPKPQKPV PLNVLQDQYK EGIKVVDIDD PDMMVDSFTM PNISHSNIDY QTLLANSDHA KFTIE PGVL PVGIDTHTAT DIYQTLIALN LDTTVNDCLD KLLNDECTES TRENALYDYY ALQLLPLQKA VRGHVLQFEW HQNSLL TNT HPNFLSKIRN INVQDALLTN QLYKNHELLK LERKKTEAVA RLKSMNKSAI NQYNRRQDKK NKRLKFGHRL IATHTNL ER DEQKRAEKKA KERLQALKAN DEEAYIKLLD QTKDTRITHL LRQTNAFLDS LTRAVKDQQK YTKEMIDSHI KEASEEVD D LSMVPKMKDE EYDDDDDNSN VDYYNVAHRI KEDIKKQPSI LVGGTLKDYQ IKGLQWMVSL FNNHLNGILA DEMGLGKTI QTISLLTYLY EMKNIRGPYL VIVPLSTLSN WSSEFAKWAP TLRTISFKGS PNERKAKQAK IRAGEFDVVL TTFEYIIKER ALLSKVKWV HMIIDEGHRM KNAQSKLSLT LNTHYHADYR LILTGTPLQN NLPELWALLN FVLPKIFNSV KSFDEWFNTP F ANTGGQDK IELSEEETLL VIRRLHKVLR PFLLRRLKKD VEKELPDKVE KVVKCKMSAL QQIMYQQMLK YRRLFIGDQN NK KMVGLRG FNNQIMQLKK ICNHPFVFEE VEDQINPTRE TNDDIWRVAG KFELLDRILP KLKATGHRVL IFFQMTQIMD IME DFLRYI NIKYLRLDGH TKSDERSELL RLFNAPDSEY LCFILSTRAG GLGLNLQTAD TVIIFDTDWN PHQDLQAQDR AHRI GQKNE VRILRLITTN SVEEVILERA YKKLDIDGKV IQAGKFDNKS TSEEQEALLR SLLDAEEERR KKRESGVEEE EELKD SEIN EILARNDEEM AVLTRMDEDR SKKEEELGVK SRLLEKSELP DIYSRDIGAE LKREESESAA VYNGRGARER KTATYN DNM SEEQWLRQFE VSDDEKNDKQ ARKQRTKKED KSEAIDGNGE IKGENIDADN DGPRINNISA EDRADTDLAM NDDDFLS KK RKAGRPRGRP KKVKLEGSEN SEPPALESSP VTGDNSPSED FMDIPKPRTA GKTSVKSART STRGRGRGRG RGRGRGRG R GRPPKARNGL DYVRTPAAAT SPIDIREKVA KQALDLYHFA LNYENEAGRK LSDIFLSKPS KALYPDYYMI IKYPVAFDN INTHIETLAY NSLKETLQDF HLIFSNARIY NTEGSVVYED SLELEKVVTK KYCEIMGDNS QLDFTEFDEQ YGTRPLVLPP VVTSSVAES FTDEADSSMT EASV

UniProtKB: Transcription regulatory protein SNF2

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Macromolecule #2: SWI/SNF chromatin-remodeling complex subunit SWI1

MacromoleculeName: SWI/SNF chromatin-remodeling complex subunit SWI1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 148.065188 KDa
SequenceString: MDFFNLNNNN NNNNTTTTTT TTNNNNTNNN NTNNNNNPAN NTNNNNSTGH SSNTNNNTNN NNTNTGASGV DDFQNFFDPK PFDQNLDSN NNNSNSNNND NNNSNTVASS TNFTSPTAVV NNAAPANVTG GKAANFIQNQ SPQFNSPYDS NNSNTNLNSL S PQAILAKN ...String:
MDFFNLNNNN NNNNTTTTTT TTNNNNTNNN NTNNNNNPAN NTNNNNSTGH SSNTNNNTNN NNTNTGASGV DDFQNFFDPK PFDQNLDSN NNNSNSNNND NNNSNTVASS TNFTSPTAVV NNAAPANVTG GKAANFIQNQ SPQFNSPYDS NNSNTNLNSL S PQAILAKN SIIDSSNLPL QAQQQLYGGN NNNNSTGIAN DNVITPHFIT NVQSISQNSS SSTPNTNSNS TPNANQQFLP FN NSASNNG NLTSNQLISN YAASNSMDRS SSASNEFVPN TSDNNNNSNN HNMRNNSNNK TSNNNNVTAV PAATPANTNN STS NANTVF SERAAMFAAL QQKQQQRFQA LQQQQQQQQN QQQQNQQPQQ QQQQQQNPKF LQSQRQQQQR SILQSLNPAL QEKI STELN NKQYELFMKS LIENCKKRNM PLQSIPEIGN RKINLFYLYM LVQKFGGADQ VTRTQQWSMV AQRLQISDYQ QLESI YFRI LLPYERHMIS QEGIKETQAK RIFLQQFLQE LLKKVQQQQQ AAALANANNN INSASSAPTP AAPGASVPAT AAPGTE AGI VPVSANTPKS LNSNININVN NNNIGQQQVK KPRKQRVKKK TKKELELERK EREDFQKRQQ KLLEDQQRQQ KLLLETK LR QQYEIELKKL PKVYKRSIVR NYKPLINRLK HYNGYDINYI SKIGEKIDSN KPIFLFAPEL GAINLHALSM SLQSKNLG E INTALNTLLV TSADSNLKIS LVKYPELLDS LAILGMNLLS NLSQNVVPYH RNTSDYYYED AGSNQYYVTQ HDKMVDKIF EKVNNNATLT PNDSNDEKVT ILVDSLTGNQ LPTPTPTEME PDLDTECFIS MQSTSPAVKQ WDLLPEPIRF LPNQFPLKIH RTPYLTSLK KIKDEIDDPF TKINTRGAED PKVLINDQLS TISMILRNIS FSDNNSRIMS RNFYLKRFIS DLLWLVLIHP E NFTCNRKI LNFKKDLVIV LSNISHLLEI ASSIDCLLIL ILVISFGQPK LNPMASSSSF GSESLTFNEF QLQWGKYQTF GV DILAKLF SLEKPNLNYF KSILLNKNTG NNLYDRNSNN NHKDKKLLRR LLNLYNDNNK NNNNRHNLLN DVVSFLFSAI PLQ QVLSQS ADPSLLIDQF SPVISQSLTS ILVIVQKILP LSNEVFEISE NNSDSNSNNN GNKDSSFNFN KNLPFVWLSS EENI GSGLL KLSEIILNIN NSTSKNTLLQ QQNYSKVLLP SINISCVQLI KCLVEKSICF ENCLNNDPEI LKKIASIPNL FPTDL EIFQ LFTNPSVDIQ IINQYQLLYN LKNDILTNLE

UniProtKB: SWI/SNF chromatin-remodeling complex subunit SWI1

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Macromolecule #3: SWI/SNF chromatin-remodeling complex subunit SNF5

MacromoleculeName: SWI/SNF chromatin-remodeling complex subunit SNF5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 102.642172 KDa
SequenceString: MNNQPQGTNS VPNSIGNIFS NIGTPSFNMA QIPQQLYQSL TPQQLQMIQQ RHQQLLRSRL QQQQQQQQQT SPPPQTHQSP PPPPQQSQP IANQSATSTP PPPPAPHNLH PQIGQVPLAP APINLPPQIA QLPLATQQQV LNKLRQQAIA KNNPQVVNAI T VAQQQVQR ...String:
MNNQPQGTNS VPNSIGNIFS NIGTPSFNMA QIPQQLYQSL TPQQLQMIQQ RHQQLLRSRL QQQQQQQQQT SPPPQTHQSP PPPPQQSQP IANQSATSTP PPPPAPHNLH PQIGQVPLAP APINLPPQIA QLPLATQQQV LNKLRQQAIA KNNPQVVNAI T VAQQQVQR QIEQQKGQQT AQTQLEQQRQ LLVQQQQQQQ LRNQIQRQQQ QQFRHHVQIQ QQQQKQQQQQ QQHQQQQQQQ QQ QQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QGQIPQSQQV PQVRSMSGQP PTNVQPTIGQ LPQLPKLNLP KYQTIQYDPP ETK LPYPTY WSDKKADTDT LLYEQIIQRD KINKYSLIRE TNGYDPFSIY GFSNKEYISR LWHTLKYYQD LKNTRMKSIT STSQ KIPSA SIWGNGYSGY GNGITNTTTR VIPQVEVGNR KHYLEDKLKV YKQAMNETSE QLVPIRLEFD QDRDRFFLRD TLLWN KNDK LIKIEDFVDD MLRDYRFEDA TREQHIDTIC QSIQEQIQEF QGNPYIELNQ DRLGGDDLRI RIKLDIVVGQ NQLIDQ FEW DISNSDNCPE EFAESMCQEL ELPGEFVTAI AHSIREQVHM YHKSLALLGY NFDGSAIEDD DIRSRMLPTI TLDDVYR PA AESKIFTPNL LQISAAELER LDKDKDRDTR RKRRQGRSNR RGMLALSGTS ASNTSMNGVH NTVAAGNASS LPPGEILL P DIADIPRTFR TPVPSTLMPG GVDVGPSVES YELRNTTTYK SRPDRPKPVS PPCYIIDHIP GHSLLLSIKL PGKVNTKEE FAAAPNDTSS GTNAMLPSPE SLKTKLNSNI RAGVTIPSIP NPIANHTVTN SPNPTLQPVI PGGAASKSVP TPSLPIAPPV APHDSEATL LTNSNNGSSN NNTQNT

UniProtKB: SWI/SNF chromatin-remodeling complex subunit SNF5

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Macromolecule #4: SWI/SNF complex subunit SWI3

MacromoleculeName: SWI/SNF complex subunit SWI3 / type: protein_or_peptide / ID: 4
Details: Residues 597-653 and 765-780 of chain F, and residues 609-655 and 763-779 of chain G are not confidently assigned
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 93.034164 KDa
SequenceString: MENTLGEGST VNASVDVDQH GNDNNSDSNA NAAVAGVANT DTAGEESQQQ DESLKDEATV PNTRDAESEA ITVTAKQQPT MQANKLDSQ ETPSTEESRA QNVFGQDNED SDNLFGETES SVSNNEANTP SIPTNPVDNE NNKPAIKEDS TIQDSNGDVK N MEDVKIQK ...String:
MENTLGEGST VNASVDVDQH GNDNNSDSNA NAAVAGVANT DTAGEESQQQ DESLKDEATV PNTRDAESEA ITVTAKQQPT MQANKLDSQ ETPSTEESRA QNVFGQDNED SDNLFGETES SVSNNEANTP SIPTNPVDNE NNKPAIKEDS TIQDSNGDVK N MEDVKIQK EEEPENNTVI EGVKEESQPD ENTKEMDEVE EDDEDDDQPM ISPDNSIFGD TKSESKQLGN TSSVANTPSE IP DAHKAEQ EDIIEKTESV DKKVDSGEER NEQEREIMND HSKSANPKKT TITRVEPETF EIPQAHEIVI PSYSKWFNLE KIH SIEVQS LPEFFTNRIP SKTPEVYMRY RNFMVNSYRL NPNEYFSVTT ARRNVSGDAA ALFRLHKFLT KWGLINYQVD SKLL PKNIE PPLTSQYSTR HDAPRGLFPF ESYKPSVQLP DMAKLKKMMN TSDSESTLYK YLKESKRKYD EITHPPSTTD DENGD KNDN GGKMNNEVST STSMTGDANL LEEGETSRPL KKVKILEQID ENWSKEDLQK LLKGIQEFGA DWYKVAKNVG NKSPEQ CIL RFLQLPIEDK FLYGDGNGKG DNDNGLGPLK YAPHLPFSKS ENPVLSTIAF LVGLVNPKTV QSMTQRAIQS AESIKSQ KE EISDQKPIEH IKEGSEIAIS SLGYRSHIFA TNEERQMNFL TNELIRLQME KLDAKLNHLK KLEKFMELER KTLERQQE N LLIQRLNFNQ NSSKIVNVLS KCLNLISDSN INNSSVAEKE EIRSQIDHFK SMLSKPETLS IGKNPFNKPN IETGENHNG QSISNENDVK PISIEAPQFY RYWSA

UniProtKB: SWI/SNF complex subunit SWI3

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Macromolecule #5: Transcription regulatory protein SNF12

MacromoleculeName: Transcription regulatory protein SNF12 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 63.947633 KDa
SequenceString: MSKVMKPSNG KGSRKSSKAA TPDTKNFFHA KKKDPVNQDK ANNASQITPT VPHSHPSDMV IPDHLAELIP ELYSFQQLVD SEKRLDHFI HLRNLHMKRM VAQWERSKLS QEFLYPHLNF PNVKFLRIFI SNVSENQPWQ MDTNNEADLM ALENATWTMR I EGRLLDNV ...String:
MSKVMKPSNG KGSRKSSKAA TPDTKNFFHA KKKDPVNQDK ANNASQITPT VPHSHPSDMV IPDHLAELIP ELYSFQQLVD SEKRLDHFI HLRNLHMKRM VAQWERSKLS QEFLYPHLNF PNVKFLRIFI SNVSENQPWQ MDTNNEADLM ALENATWTMR I EGRLLDNV QANDPAREKF SSFIESIVVD FKNKENDNVP STKFNAAPEE NATEGPSDKK LNLNLPLQFS LPNGDNSTTT NT DQNNATM GEETAKKDMS STTPKLESVK WQYDPNNPVD FDGLDIKRVG SENVECTISI LRKSSPEEPF MSYSPQLTAI IGL KSGTSH DAIFSIYKYI HLNELLTNDE SAFENLMGNR NNHNSNTSTS KMLDAASSQV SIVKLDTQLI TLLPSSLKES SPDT MKLTD LLSLINSTHL LPLQPIEIDY TVRVDKASTY GELVLDIEVP DVNALKFNNT QRESQIGAAE LNENARELEQ IKPKI ALQD KEITSVLSNL HESNKRYRFF KKISEDPVKA LNECIASTSN ALKVLSGDEG YNEDMVRRAN FYKENEAMLR ENIEVI LSN GRM

UniProtKB: Transcription regulatory protein SNF12

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Macromolecule #6: Transcription regulatory protein SNF6

MacromoleculeName: Transcription regulatory protein SNF6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.565189 KDa
SequenceString: MGVIKKKRSH HGKASRQQYY SGVQVGGVGS MGAINNNIPS LTSFAEENNY QYGYSGSSAG MNGRSLTYAQ QQLNKQRQDF ERVRLRPEQ LSNIIHDESD TISFRSNLLK NFISSNDAFN MLSLTTVPCD RIEKSRLFSE KTIRYLMQKQ H(UNK)(UNK) (UNK)(UNK)(UNK) ...String:
MGVIKKKRSH HGKASRQQYY SGVQVGGVGS MGAINNNIPS LTSFAEENNY QYGYSGSSAG MNGRSLTYAQ QQLNKQRQDF ERVRLRPEQ LSNIIHDESD TISFRSNLLK NFISSNDAFN MLSLTTVPCD RIEKSRLFSE KTIRYLMQKQ H(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

UniProtKB: Transcription regulatory protein SNF6

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Macromolecule #7: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.720042 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)

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Macromolecule #8: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 2.400951 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #9: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 1.549902 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #10: SWI/SNF global transcription activator complex subunit SWP82

MacromoleculeName: SWI/SNF global transcription activator complex subunit SWP82
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.08172 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #11: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 2.571161 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
Details: 10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 76.5 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: Ab initio from Cryosparc
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 61518
FSC plot (resolution estimation)

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