[English] 日本語
Yorodumi
- PDB-6k15: RSC substrate-recruitment module -

+
Open data


ID or keywords:

Loading...

-
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 / histone H2A reader activity / : / : / : / regulation of nuclear cell cycle DNA replication / histone H3 reader activity / plasmid maintenance / CENP-A containing chromatin assembly / DNA translocase activity ...regulation of sporulation resulting in formation of a cellular spore / histone H2A reader activity / : / : / : / regulation of nuclear cell cycle DNA replication / histone H3 reader activity / plasmid maintenance / CENP-A containing chromatin assembly / DNA translocase activity / nucleosome array spacer activity / histone H3K14ac reader activity / RSC-type complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / SWI/SNF complex / UV-damage excision repair / sister chromatid cohesion / sporulation resulting in formation of a cellular spore / nuclear chromosome / rRNA transcription / histone H4 reader activity / chromosome, centromeric region / nucleosome binding / cytoskeleton organization / DNA helicase activity / helicase activity / meiotic cell cycle / transcription coregulator activity / chromosome segregation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / chromatin DNA binding / base-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / double-strand break repair / heterochromatin formation / histone binding / sequence-specific DNA binding / DNA helicase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / structural molecule activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
Similarity search - Function
: / Rsc1/Rsc2, bromodomain / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / : / : / RSC4 Ig-like domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / DNA-binding RFX-type winged-helix domain ...: / Rsc1/Rsc2, bromodomain / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / : / : / RSC4 Ig-like domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / : / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Remodelling complex subunit Rsc/polybromo / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Bromo adjacent homology domain / BAH domain / SWIB/MDM2 domain superfamily / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / SANT domain / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / 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
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
Similarity search - Component
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.
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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9905
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
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

-
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

-
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

-
Non-polymers , 1 types, 1 molecules

#13: Chemical ChemComp-ZN / ZINC ION


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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