5TGC

Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase.

Turegun, B.Baker, R.W.Leschziner, A.E.Dominguez, R.

(2018) Commun Biol 1

  • DOI: https://doi.org/10.1038/s42003-017-0002-6
  • Primary Citation of Related Structures:  
    5TGC

  • PubMed Abstract: 

    The catalytic subunits of SWI/SNF-family and INO80-family chromatin remodelers bind actin and actin-related proteins (Arps) through an N-terminal helicase/SANT-associated (HSA) domain. Between the HSA and ATPase domains lies a conserved post-HSA (pHSA) domain. The HSA domain of Sth1, the catalytic subunit of the yeast SWI/SNF-family remodeler RSC, recruits the Rtt102-Arp7/9 heterotrimer. Rtt102-Arp7/9 regulates RSC function, but the mechanism is unclear. We show that the pHSA domain interacts directly with another conserved region of the catalytic subunit, protrusion-1. Rtt102-Arp7/9 binding to the HSA domain weakens this interaction and promotes the formation of stable, monodisperse complexes with DNA and nucleosomes. A crystal structure of Rtt102-Arp7/9 shows that ATP binds to Arp7 but not Arp9. However, Arp7 does not hydrolyze ATP. Together, the results suggest that Rtt102 and ATP stabilize a conformation of Arp7/9 that potentiates binding to the HSA domain, which releases intramolecular interactions within Sth1 and controls DNA and nucleosome binding.


  • Organizational Affiliation

    Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 728 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA, 19104-6085, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 7
A, D
490Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARP7
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12406 
Go to UniProtKB:  Q12406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12406
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP9
B, E
467Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARP9
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05123 
Go to UniProtKB:  Q05123
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05123
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102
C, F
158Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RTT102
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53330 
Go to UniProtKB:  P53330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53330
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.387α = 109.03
b = 87.982β = 104.64
c = 105.43γ = 96.2
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SAINTdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01_GM073791

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-10-04
    Changes: Data collection, Database references, Refinement description