6KW4

The ClassB RSC-Nucleosome Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.55 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.aay0033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RSC complex remodels chromatin structure and regulates gene transcription. We report the cryoEM structure of yeast RSC bound to the nucleosome. RSC is delineated into the ATPase motor, the actin-related-protein (ARP) module, and the substrate-rec ...

    The RSC complex remodels chromatin structure and regulates gene transcription. We report the cryoEM structure of yeast RSC bound to the nucleosome. RSC is delineated into the ATPase motor, the actin-related-protein (ARP) 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. Together, our findings shed light on RSC assembly and functionality, and provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers.


    Organizational Affiliation

    School of Life Science, Tsinghua University, Beijing 100084, P.R. China.,Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA. zhucheng_chen@tsinghua.edu.cn gaon@pku.edu.cn brad.cairns@hci.utah.edu.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, P.R. China. zhucheng_chen@tsinghua.edu.cn gaon@pku.edu.cn brad.cairns@hci.utah.edu.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Beijing 100084, China.,Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China. zhucheng_chen@tsinghua.edu.cn gaon@pku.edu.cn brad.cairns@hci.utah.edu.,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing 100084, China.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, P.R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
N, Q
136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, R
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
O, S
130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 7
f
477Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARP7 (SWP61)
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12406
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Regulator of Ty1 transposition protein 102
h
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RTT102
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53330
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC7
F
435Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NPL6 (RSC7)
Find proteins for P32832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32832
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC8
H, D
557Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC8 (SWH3)
Find proteins for P43609 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43609
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC9
M
581Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC9
Find proteins for Q03124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03124
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC6
I
483Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC6
Find proteins for P25632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25632
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit SFH1
G
426Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SFH1
Find proteins for Q06168 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06168
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC58
A
502Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC58
Find proteins for Q07979 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07979
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein STH1/NPS1
J, V, Y
1359Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: STH1 (NPS1)
EC: 3.6.4.12
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32597
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
High temperature lethal protein 1
E
78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTL1 (DRT1)
Find proteins for Q9URQ5 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q9URQ5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC30
C
883Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC30
Find proteins for P38781 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38781
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC3
K
885Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC3
Find proteins for Q06639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06639
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC4
X
625Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC4
Find proteins for Q02206 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02206
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC2
L
889Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSC2
Find proteins for Q06488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06488
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Histone H4
P, T
126Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP9
g
467Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARP9 (SWP59)
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05123
Entity ID: 4
MoleculeChainsLengthOrganism
DNA 167U167Homo sapiens
Entity ID: 5
MoleculeChainsLengthOrganism
DNA 167W167Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.55 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references