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 

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Ligand Structure Quality Assessment 


This is version 1.5 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: 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 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. droberto@pennmedicine.upenn.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 7A, D490Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARP7
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12406 
Go to UniProtKB:  Q12406
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP9B, E467Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARP9
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05123 
Go to UniProtKB:  Q05123
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102C, F158Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RTT102
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53330 
Go to UniProtKB:  P53330
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
G [auth A], J [auth D]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B], I [auth B], K [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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