6KW3

The ClassA RSC-Nucleosome Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.13 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the RSC complex bound to the nucleosome.

Ye, Y.Wu, H.Chen, K.Clapier, C.R.Verma, N.Zhang, W.Deng, H.Cairns, B.R.Gao, N.Chen, Z.

(2019) Science 366: 838-843

  • DOI: https://doi.org/10.1126/science.aay0033
  • Primary Citation of Related Structures:  
    6K15, 6KW3, 6KW4

  • PubMed 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 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.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, P.R. China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4A [auth B],
E [auth R]
103Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2B [auth N],
D [auth Q]
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AC [auth O],
F [auth S]
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein STH1/NPS1BA [auth Y],
I [auth W],
S [auth J]
1,359Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 7J [auth f]477Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102K [auth h]157Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC7L [auth F]435Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC8M [auth H],
N [auth D]
557Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC9O [auth M]581Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC6P [auth I]483Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit SFH1Q [auth G]426Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC58R [auth A]502Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
High temperature lethal protein 1T [auth E]78Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC30U [auth C]883Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC3V [auth K]885Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC4W [auth X]625Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC2X [auth L]889Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4Y [auth T],
Z [auth P]
126Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18028549mg
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP9AA [auth g]467Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA 167G [auth U]167Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA 167H [auth V]167Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth H]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.13 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references