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- EMDB-0777: The ClassA RSC-Nucleosome Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0777
TitleThe ClassA RSC-Nucleosome Complex
Map data
SampleRSC
  • (Histone H4) x 2
  • Histone H3.2
  • Histone H2A
  • (nucleic-acidNucleic acid) x 2
  • Nuclear protein STH1/NPS1
  • Actin-related protein 7
  • Regulator of Ty1 transposition protein 102
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • (Chromatin structure-remodeling complex protein ...) x 5
  • High temperature lethal protein 1
  • Actin-like protein ARP9
  • ligand
Function / homology
Function and homology information


regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / transfer RNA gene-mediated silencing / plasmid maintenance / DNA translocase activity / structural constituent of postsynaptic actin cytoskeleton / nucleosome mobilization / RSC-type complex / nucleosome positioning ...regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / transfer RNA gene-mediated silencing / plasmid maintenance / DNA translocase activity / structural constituent of postsynaptic actin cytoskeleton / nucleosome mobilization / RSC-type complex / nucleosome positioning / UV-damage excision repair / nucleosome disassembly / SWI/SNF complex / NuA4 histone acetyltransferase complex / sister chromatid cohesion / ATP-dependent chromatin remodeling / rRNA transcription / synaptic vesicle endocytosis / sporulation resulting in formation of a cellular spore / chromosome, centromeric region / histone H4 acetylation / DNA-dependent ATPase activity / cytoskeleton organization / transcription elongation from RNA polymerase II promoter / DNA-templated transcription, initiation / helicase activity / DNA helicase / DNA helicase activity / actin filament / lysine-acetylated histone binding / positive regulation of transcription elongation from RNA polymerase II promoter / meiotic cell cycle / chromosome segregation / rRNA processing / double-strand break repair via homologous recombination / nucleosome / chromatin DNA binding / double-strand break repair / cellular response to hydrogen peroxide / base-excision repair / double-strand break repair via nonhomologous end joining / chromatin organization / histone binding / G2/M transition of mitotic cell cycle / transcription regulatory region DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / sequence-specific DNA binding / ATPase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / cellular response to DNA damage stimulus / chromatin binding / regulation of transcription, DNA-templated / structural molecule activity / protein heterodimerization activity / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
Bromo adjacent homology (BAH) domain / Helicase superfamily 1/2, ATP-binding domain / Transcription regulator protein Rtt102 / SANT domain / Bromodomain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase, C-terminal / Helicase/SANT-associated domain / Histone H4 / Zn(2)-C6 fungal-type DNA-binding domain ...Bromo adjacent homology (BAH) domain / Helicase superfamily 1/2, ATP-binding domain / Transcription regulator protein Rtt102 / SANT domain / Bromodomain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase, C-terminal / Helicase/SANT-associated domain / Histone H4 / Zn(2)-C6 fungal-type DNA-binding domain / SNF2-related, N-terminal domain / Histone H2A / DNA-binding RFX-type winged-helix domain / Actin family / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / TATA box binding protein associated factor (TAF) / Histone-fold / Homeobox-like domain superfamily / SNF5/SMARCB1/INI1 / Histone H2A/H2B/H3 / Bromodomain, conserved site / Histone H4, conserved site / Histone H2B / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / SANT/Myb domain / SNF2-like, N-terminal domain superfamily / Remodelling complex subunit Rsc/polybromo / SWIB/MDM2 domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily / Zinc finger, ZZ-type / SWIRM domain / Rsc1/Rsc2, bromodomain / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / SMARCC, C-terminal / Snf2, ATP coupling domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4
Chromatin structure-remodeling complex subunit RSC9 / Histone H2A / Actin-related protein 7 / Chromatin structure-remodeling complex protein RSC58 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex subunit SFH1 / Actin-like protein ARP9 / Regulator of Ty1 transposition protein 102 / Chromatin structure-remodeling complex subunit RSC4 ...Chromatin structure-remodeling complex subunit RSC9 / Histone H2A / Actin-related protein 7 / Chromatin structure-remodeling complex protein RSC58 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex subunit SFH1 / Actin-like protein ARP9 / Regulator of Ty1 transposition protein 102 / Chromatin structure-remodeling complex subunit RSC4 / un:p84233: / un:p62799: / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex subunit RSC7 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex protein RSC6 / Histone H4 / High temperature lethal protein 1
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Xenopus laevis (African clawed frog) / Homo sapiens (human) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.13 Å
AuthorsYe YP / Wu H / Chen KJ / Verma N / Cairns B / Gao N / Chen ZC
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 ReportPDB-ID: 6kw3

SummaryFull reportAbout validation report
History
DepositionSep 5, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6kw3
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0777.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.14 Å/pix.
x 180 pix.
= 385.2 Å
2.14 Å/pix.
x 180 pix.
= 385.2 Å
2.14 Å/pix.
x 180 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.14 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.01342345 - 0.11891705
Average (Standard dev.)0.0012106178 (±0.005624704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.142.142.14
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0130.1190.001

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Supplemental data

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Sample components

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Entire RSC

EntireName: RSC / Number of components: 23

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Component #1: protein, RSC

ProteinName: RSC / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.421101 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.109436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: nucleic-acid, DNA 167

nucleic acidName: DNA 167 / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DT)(DA)(DG)
MassTheoretical: 51.421781 kDa
SourceSpecies: Homo sapiens (human)

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Component #6: nucleic-acid, DNA 167

nucleic acidName: DNA 167 / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DT)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DA)(DT)(DC)
MassTheoretical: 51.683922 kDa
SourceSpecies: Homo sapiens (human)

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Component #7: protein, Nuclear protein STH1/NPS1

ProteinName: Nuclear protein STH1/NPS1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 156.982406 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, Actin-related protein 7

ProteinName: Actin-related protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.863016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, Regulator of Ty1 transposition protein 102

ProteinName: Regulator of Ty1 transposition protein 102 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.817615 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Chromatin structure-remodeling complex subunit RSC7

ProteinName: Chromatin structure-remodeling complex subunit RSC7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.71652 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Chromatin structure-remodeling complex protein RSC8

ProteinName: Chromatin structure-remodeling complex protein RSC8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 63.253965 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Chromatin structure-remodeling complex subunit RSC9

ProteinName: Chromatin structure-remodeling complex subunit RSC9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.289309 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Chromatin structure-remodeling complex protein RSC6

ProteinName: Chromatin structure-remodeling complex protein RSC6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.222691 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Chromatin structure-remodeling complex subunit SFH1

ProteinName: Chromatin structure-remodeling complex subunit SFH1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.83318 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Chromatin structure-remodeling complex protein RSC58

ProteinName: Chromatin structure-remodeling complex protein RSC58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.871309 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, High temperature lethal protein 1

ProteinName: High temperature lethal protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.192524 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Chromatin structure-remodeling complex protein RSC30

ProteinName: Chromatin structure-remodeling complex protein RSC30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.448211 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, Chromatin structure-remodeling complex protein RSC3

ProteinName: Chromatin structure-remodeling complex protein RSC3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.833961 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, Chromatin structure-remodeling complex subunit RSC4

ProteinName: Chromatin structure-remodeling complex subunit RSC4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.372375 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, Chromatin structure-remodeling complex subunit RSC2

ProteinName: Chromatin structure-remodeling complex subunit RSC2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.443664 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.925202 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #22: protein, Actin-like protein ARP9

ProteinName: Actin-like protein ARP9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.13193 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 45077
3D reconstructionResolution: 7.13 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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