6TDA

Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome.

Wagner, F.R.Dienemann, C.Wang, H.Stutzer, A.Tegunov, D.Urlaub, H.Cramer, P.

(2020) Nature 579: 448-451

  • DOI: 10.1038/s41586-020-2088-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Chromatin-remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs) 1,2 . In the yeast Saccharomyces cerevisiae, the essential SWI/SNF complex RSC 3 ...

    Chromatin-remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs) 1,2 . In the yeast Saccharomyces cerevisiae, the essential SWI/SNF complex RSC 3 contains 16 subunits, including the ATP-dependent DNA translocase Sth1 4,5 . RSC removes nucleosomes from promoter regions 6,7 and positions the specialized +1 and -1 nucleosomes that flank NDRs 8,9 . Here we present the cryo-electron microscopy structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and actin-related protein (ARP) modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements 8,10,11 that influence RSC functionality 12 . The ATPase and arm modules sandwich the nucleosome disc with the Snf2 ATP-coupling (SnAC) domain and the finger helix, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity 5 . The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer 13 .


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit SFH1
K
426Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SFH1YLR321CL8543.4
Find proteins for Q06168 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC8,Chromatin structure-remodeling complex protein RSC8
L
1114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC8
Find proteins for P43609 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC7
M
435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NPL6RSC7YMR091CYM9582.16C
Find proteins for P32832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32832
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC9
N
581Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC9YML127WYM4987.08
Find proteins for Q03124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03124
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC58
P
502Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC58YLR033W
Find proteins for Q07979 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
High temperature lethal protein 1
Q
78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTL1DRT1YCR020W-B
Find proteins for Q9URQ5 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC4
R
625Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC4YKR008WYK107
Find proteins for Q02206 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 7
T
477Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP7SWP61YPR034WYP9367.14
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP9
U
467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP9SWP59YMR033WYM9973.07
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Regulator of Ty1 transposition protein 102
V
157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT102YGR275WG9378
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown protein
X
383Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC6
O
483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC6YCR052WYCR52W
Find proteins for P25632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein STH1/NPS1
S
1359Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32597
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Entity ID: 5
MoleculeChainsLengthOrganism
DNA-II237synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA-JJ237synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
TL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)--
European Research Council (ERC)--
Volkswagen Foundation--

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references