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- EMDB-21107: RSC core -

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Basic information

Entry
Database: EMDB / ID: EMD-21107
TitleRSC core
Map data
SampleRemodeling the Structure of Chromatin (RSC)
  • High temperature lethal protein 1
  • (Chromatin structure-remodeling complex protein ...) x 6
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • Nuclear protein STH1/NPS1
  • (Unknown protein) x 2
  • (Unknown Protein) x 3
  • ligand
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 / nucleosome disassembly / UV-damage excision repair / nucleosome positioning ...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 / nucleosome disassembly / UV-damage excision repair / nucleosome positioning / 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 / transcription elongation from RNA polymerase II promoter / cytoskeleton organization / meiotic cell cycle / positive regulation of transcription elongation from RNA polymerase II promoter / chromosome segregation / lysine-acetylated histone binding / base-excision repair / double-strand break repair via homologous recombination / double-strand break repair / transcription coregulator activity / rRNA processing / cellular response to hydrogen peroxide / helicase activity / DNA helicase / DNA helicase activity / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / ATPase activity / chromatin binding / regulation of transcription by RNA polymerase II / regulation of transcription, DNA-templated / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Winged helix-like DNA-binding domain superfamily / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Chromatin-remodeling complex component Sfh1/SNF5 / P-loop containing nucleoside triphosphate hydrolase / Helicase superfamily 1/2, ATP-binding domain / Helicase/SANT-associated domain / Snf2, ATP coupling domain / SNF2-related domain / Zinc finger, ZZ-type ...Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Winged helix-like DNA-binding domain superfamily / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Chromatin-remodeling complex component Sfh1/SNF5 / P-loop containing nucleoside triphosphate hydrolase / Helicase superfamily 1/2, ATP-binding domain / Helicase/SANT-associated domain / Snf2, ATP coupling domain / SNF2-related domain / Zinc finger, ZZ-type / SANT/Myb domain / Bromo adjacent homology (BAH) domain / Zn(2)-C6 fungal-type DNA-binding domain / Bromodomain / Bromodomain, conserved site / Rsc1/Rsc2, bromodomain / SMARCC, C-terminal / SANT domain / Remodelling complex subunit Rsc/polybromo / Homeobox-like domain superfamily / Bromo adjacent homology (BAH) domain superfamily / Zinc finger, ZZ-type superfamily / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / Bromodomain-like superfamily / Chromatin structure-remodeling complex protein Rsc14 / SNF2-like, N-terminal domain superfamily / SWIRM domain / SNF5/SMARCB1/INI1 / SWIB/MDM2 domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / DNA-binding RFX-type winged-helix domain / Helicase, C-terminal
Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC9 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC2 ...Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC9 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex protein RSC58 / High temperature lethal protein 1
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsPatel AB / Moore CM / Greber BJ / Nogales E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24GM129547 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127018 United States
CitationJournal: Elife / Year: 2019
Title: Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.
Authors: Avinash B Patel / Camille M Moore / Basil J Greber / Jie Luo / Stefan A Zukin / Jeff Ranish / Eva Nogales /
Abstract: Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The RSC (emodeling the tructure of hromatin) complex, a ...Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The RSC (emodeling the tructure of hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.
Validation ReportPDB-ID: 6v8o

SummaryFull reportAbout validation report
History
DepositionDec 11, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v8o
  • Surface level: 0.03
  • 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_21107.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 288 pix.
= 414.432 Å
1.44 Å/pix.
x 288 pix.
= 414.432 Å
1.44 Å/pix.
x 288 pix.
= 414.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.439 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.12098607 - 0.23140849
Average (Standard dev.)-0.000035609 (±0.0048622275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 414.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4391.4391.439
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z414.432414.432414.432
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1210.231-0.000

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Supplemental data

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Segmentation: #1

Fileemd_21107_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: RSC core structure

Fileemd_21107_half_map_1.map
AnnotationRSC core structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: RSC core structure

Fileemd_21107_half_map_2.map
AnnotationRSC core structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Remodeling the Structure of Chromatin (RSC)

EntireName: Remodeling the Structure of Chromatin (RSC) / Number of components: 20

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Component #1: protein, Remodeling the Structure of Chromatin (RSC)

ProteinName: Remodeling the Structure of Chromatin (RSC) / Recombinant expression: No
MassTheoretical: 1.1 MDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #2: 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 #3: protein, Chromatin structure-remodeling complex protein RSC14

ProteinName: Chromatin structure-remodeling complex protein RSC14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.825398 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: 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 #5: 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 #6: protein, Chromatin structure-remodeling complex protein RSC3

ProteinName: Chromatin structure-remodeling complex protein RSC3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.819938 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: 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 #8: protein, Chromatin structure-remodeling complex protein RSC8

ProteinName: Chromatin structure-remodeling complex protein RSC8 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 63.253965 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: 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 #10: 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 #11: 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 #12: 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 #13: protein, Nuclear protein STH1/NPS1

ProteinName: Nuclear protein STH1/NPS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 156.982406 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: 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 #15: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.400951 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, Unknown Protein

ProteinName: Unknown Protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.635006 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.209482 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, Unknown Protein

ProteinName: Unknown Protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.294587 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, Unknown Protein

ProteinName: Unknown Protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.188154 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: 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: Particle / Method: cryo EM
Sample solutionpH: 7.9
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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1920066
3D reconstructionSoftware: RELION / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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