6VZ4

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into assembly and function of the RSC chromatin remodeling complex.

Baker, R.W.Reimer, J.M.Carman, P.J.Turegun, B.Arakawa, T.Dominguez, R.Leschziner, A.E.

(2021) Nat Struct Mol Biol 28: 71-80

  • DOI: 10.1038/s41594-020-00528-8
  • Primary Citation of Related Structures:  
    6VZ4, 6VZG

  • PubMed Abstract: 
  • SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102 ...

    SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT-associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.


    Organizational Affiliation

    Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA. aleschziner@health.ucsd.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E136Xenopus laevisMutation(s): 0 
Gene Names: hist1h3gh3c8H3lh3c8.S
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Find proteins for Q92133 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD, H125Xenopus laevisMutation(s): 0 
Gene Names: H2BXELAEV_18028547mg
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear protein STH1/NPS1K813Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
UniProt
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 7L477Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP7SWP61YPR034WYP9367.14
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP9M467Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARP9
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102N157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT102YGR275WG9378
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (185-MER)I185synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (185-MER)J185synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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R [auth L]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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P [auth K]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

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Q [auth K]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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O [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 States5R01GM092895-08

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references