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- PDB-6k15: RSC substrate-recruitment module -

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Basic information

Entry
Database: PDB / ID: 6k15
TitleRSC substrate-recruitment module
Components
  • (Chromatin structure-remodeling complex protein ...) x 5
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • High temperature lethal protein 1
  • Nuclear protein STH1/NPS1
KeywordsDNA BINDING PROTEIN / chromatin remodeler / SWI/SNF family
Function / homology
Function and homology information


regulation of sporulation resulting in formation of a cellular spore / regulation of nuclear cell cycle DNA replication / chromatin remodeling at centromere / plasmid maintenance / transfer RNA gene-mediated silencing / RSC-type complex / DNA translocase activity / UV-damage excision repair / nucleosome positioning / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / regulation of nuclear cell cycle DNA replication / chromatin remodeling at centromere / plasmid maintenance / transfer RNA gene-mediated silencing / RSC-type complex / DNA translocase activity / UV-damage excision repair / nucleosome positioning / nucleosome disassembly / SWI/SNF complex / sister chromatid cohesion / ATP-dependent chromatin remodeling / rRNA transcription / sporulation resulting in formation of a cellular spore / chromosome, centromeric region / DNA-dependent ATPase activity / cytoskeleton organization / transcription elongation from RNA polymerase II promoter / meiotic cell cycle / positive regulation of transcription elongation from RNA polymerase II promoter / chromosome segregation / lysine-acetylated histone binding / double-strand break repair / double-strand break repair via homologous recombination / base-excision repair / helicase activity / rRNA processing / DNA helicase / DNA helicase activity / cellular response to hydrogen peroxide / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / histone binding / chromatin remodeling / sequence-specific DNA binding / transcription regulatory region sequence-specific DNA binding / ATPase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA repair / regulation of transcription by RNA polymerase II / chromatin binding / regulation of transcription, DNA-templated / host cell nucleus / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
BAH domain / Helicase superfamily 1/2, ATP-binding domain / SMARCC, C-terminal / Snf2, ATP coupling domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain ...BAH domain / Helicase superfamily 1/2, ATP-binding domain / SMARCC, C-terminal / Snf2, ATP coupling domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Winged helix-like DNA-binding domain superfamily / Homeobox-like domain superfamily / SWIRM domain / SNF5/SMARCB1/INI1 / DNA-binding RFX-type winged-helix domain / Helicase, C-terminal / Bromodomain / Zn(2)-C6 fungal-type DNA-binding domain / SANT/Myb domain / Rsc1/Rsc2, bromodomain / Bromodomain-like superfamily / SNF2-related, N-terminal domain / Zinc finger, ZZ type / Snf2-ATP coupling, chromatin remodelling complex / HSA / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / SNF5 / SMARCB1 / INI1 / Chromatin remodelling complex Rsc7/Swp82 subunit / SWIRM-associated region 1 / SWIRM domain / Myb-like DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Fungal Zn(2)-Cys(6) binuclear cluster domain / Bromodomain / Bromo adjacent homology (BAH) domain superfamily / Zinc finger, ZZ-type superfamily / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / SNF2-like, N-terminal domain superfamily / Remodelling complex subunit Rsc/polybromo / SWIB/MDM2 domain superfamily / Zinc finger, ZZ-type / Bromo adjacent homology (BAH) domain
Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex subunit RSC7 / Nuclear protein STH1/NPS1 / High temperature lethal protein 1 / Chromatin structure-remodeling complex protein RSC6 / Chromatin structure-remodeling complex protein RSC58 / Chromatin structure-remodeling complex protein RSC3 ...Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex subunit RSC7 / Nuclear protein STH1/NPS1 / High temperature lethal protein 1 / Chromatin structure-remodeling complex protein RSC6 / Chromatin structure-remodeling complex protein RSC58 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex subunit RSC9
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYe, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C.
CitationJournal: Science / Year: 2019
Title: Structure of the RSC complex bound to the nucleosome.
Authors: Youpi Ye / Hao Wu / Kangjing Chen / Cedric R Clapier / Naveen Verma / Wenhao Zhang / Haiteng Deng / Bradley R Cairns / Ning Gao / Zhucheng Chen /
Abstract: The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into ...The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
F: Chromatin structure-remodeling complex subunit RSC7
H: Chromatin structure-remodeling complex protein RSC8
D: Chromatin structure-remodeling complex protein RSC8
M: Chromatin structure-remodeling complex subunit RSC9
I: Chromatin structure-remodeling complex protein RSC6
G: Chromatin structure-remodeling complex subunit SFH1
A: Chromatin structure-remodeling complex protein RSC58
J: Nuclear protein STH1/NPS1
E: High temperature lethal protein 1
C: Chromatin structure-remodeling complex protein RSC30
K: Chromatin structure-remodeling complex protein RSC3
X: Chromatin structure-remodeling complex subunit RSC4
L: Chromatin structure-remodeling complex subunit RSC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)946,77914
Polymers946,71413
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules FMGXL

#1: Protein Chromatin structure-remodeling complex subunit RSC7 / Nuclear protein localization protein 6 / Remodel the structure of chromatin complex subunit 7


Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P32832
#3: Protein Chromatin structure-remodeling complex subunit RSC9 / RSC complex subunit RSC9 / Remodel the structure of chromatin complex subunit 9


Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q03124
#5: Protein Chromatin structure-remodeling complex subunit SFH1 / RSC complex subunit SFH1 / SNF5 homolog 1


Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06168
#11: Protein Chromatin structure-remodeling complex subunit RSC4 / RSC complex subunit RSC4 / Remodel the structure of chromatin complex subunit 4


Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q02206
#12: Protein Chromatin structure-remodeling complex subunit RSC2 / RSC complex subunit RSC2 / Remodel the structure of chromatin complex subunit 2


Mass: 102443.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06488

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Chromatin structure-remodeling complex protein ... , 5 types, 6 molecules HDIACK

#2: Protein Chromatin structure-remodeling complex protein RSC8 / Remodel the structure of chromatin complex subunit 8 / SWI3 homolog


Mass: 63253.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P43609
#4: Protein Chromatin structure-remodeling complex protein RSC6 / Remodel the structure of chromatin complex subunit 6


Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P25632
#6: Protein Chromatin structure-remodeling complex protein RSC58 / Remodel the structure of chromatin complex subunit 58


Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q07979
#9: Protein Chromatin structure-remodeling complex protein RSC30 / Remodel the structure of chromatin complex subunit 30


Mass: 101448.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P38781
#10: Protein Chromatin structure-remodeling complex protein RSC3 / Remodel the structure of chromatin complex subunit 3


Mass: 101833.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06639

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Protein , 2 types, 2 molecules JE

#7: Protein Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 156982.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32597, DNA helicase
#8: Protein High temperature lethal protein 1 / Chromatin structure-remodeling complex protein HTL1


Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q9URQ5

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Non-polymers , 1 types, 1 molecules

#13: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RSC / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280000 / Symmetry type: POINT

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