6V8O

RSC core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Patel, A.B.Moore, C.M.Greber, B.J.Luo, J.Zukin, S.A.Ranish, J.Nogales, E.

(2019) Elife 8

  • DOI: 10.7554/eLife.54449
  • Primary Citation of Related Structures:  
    6V92, 6V8O

  • PubMed Abstract: 
  • Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC ( R emodeling the S tructure of C hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair ...

    Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC ( R emodeling the S tructure of C hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High temperature lethal protein 1 C78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTL1DRT1YCR020W-B
Find proteins for Q9URQ5 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC14 D180Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LDB7RSC14YBL006CYBL0322
Find proteins for P38210 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC7 E435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NPL6RSC7YMR091CYM9582.16C
Find proteins for P32832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC2 F889Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC2YLR357WL9638.1
Find proteins for Q06488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC3 G885Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC3YDR303CD9740.13
Find proteins for Q06639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC4 H625Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC4YKR008WYK107
Find proteins for Q02206 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC8 IJKL557Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC8SWH3YFR037C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC6 M483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC6YCR052WYCR52W
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Entity ID: 9
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Chromatin structure-remodeling complex subunit RSC9 N581Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC9YML127WYM4987.08
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC58 O502Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC58YLR033W
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Entity ID: 11
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Chromatin structure-remodeling complex subunit SFH1 Q426Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SFH1YLR321CL8543.4
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Entity ID: 12
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Nuclear protein STH1/NPS1 R1359Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC30 S883Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC30YHR056C
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown protein 228Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown Protein 3419Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown protein 514Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown Protein 615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown Protein 749Saccharomyces cerevisiae S288CMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM63072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM127018
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesU24GM129547

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release