[English] 日本語
Yorodumi
- EMDB-9905: RSC substrate-recruitment module -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9905
TitleRSC substrate-recruitment module
Map data
SampleRSC
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • (Chromatin structure-remodeling complex protein ...) x 5
  • Nuclear protein STH1/NPS1
  • High temperature lethal protein 1
  • 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 / DNA translocase activity / plasmid maintenance / RSC-type complex / nucleosome positioning / UV-damage excision repair / nucleosome disassembly ...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 / DNA translocase activity / plasmid maintenance / RSC-type complex / nucleosome positioning / UV-damage excision repair / 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 / helicase activity / DNA helicase / DNA helicase activity / lysine-acetylated histone binding / positive regulation of transcription elongation from RNA polymerase II promoter / meiotic cell cycle / chromosome segregation / rRNA processing / chromatin DNA binding / double-strand break repair / double-strand break repair via homologous recombination / cellular response to hydrogen peroxide / base-excision repair / double-strand break repair via nonhomologous end joining / 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 / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
Zinc finger, ZZ-type / P-loop containing nucleoside triphosphate hydrolase / DNA-binding RFX-type winged-helix domain / SNF5/SMARCB1/INI1 / SWIRM domain / Zn(2)-C6 fungal-type DNA-binding domain / Homeobox-like domain superfamily / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Helicase superfamily 1/2, ATP-binding domain / SANT/Myb domain ...Zinc finger, ZZ-type / P-loop containing nucleoside triphosphate hydrolase / DNA-binding RFX-type winged-helix domain / SNF5/SMARCB1/INI1 / SWIRM domain / Zn(2)-C6 fungal-type DNA-binding domain / Homeobox-like domain superfamily / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Helicase superfamily 1/2, ATP-binding domain / SANT/Myb domain / Helicase/SANT-associated domain / Bromodomain / Bromo adjacent homology (BAH) domain / SANT domain / Bromodomain, conserved site / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase, C-terminal / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / Remodelling complex subunit Rsc/polybromo / SNF2-related, N-terminal domain / Snf2, ATP coupling domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / SWIB/MDM2 domain superfamily / SNF2-like, N-terminal domain superfamily / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily / Rsc1/Rsc2, bromodomain / SMARCC, C-terminal
Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / 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 RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / 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 S288c (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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: 6k15

SummaryFull reportAbout validation report
History
DepositionMay 9, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6k15
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_9905.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å
1.07 Å/pix.
x 360 pix.
= 385.2 Å
1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.055208553 - 0.09196134
Average (Standard dev.)0.0001682169 (±0.0018277868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0550.0920.000

-
Supplemental data

-
Sample components

+
Entire RSC

EntireName: RSC / Number of components: 14

+
Component #1: protein, RSC

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

+
Component #2: 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: S288c

+
Component #3: 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: S288c

+
Component #4: 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: S288c

+
Component #5: 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: S288c

+
Component #6: 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: S288c

+
Component #7: 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: S288c

+
Component #8: 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: S288c

+
Component #9: 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: S288c

+
Component #10: 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: S288c

+
Component #11: 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: S288c

+
Component #12: 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: S288c

+
Component #13: 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: S288c

+
Component #14: ligand, ZINC ION

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

-
Experimental details

-
Sample preparation

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

-
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)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 280000
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more