5TGC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


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

  • 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 (pHS ...

    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.,Department of Cellular and Molecular Medicine, School of Medicine, and Section of Molecular Biology, Division of Biological Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 7
A, D
490Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARP7 (SWP61)
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12406
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP9
B, E
467Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARP9 (SWP59)
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05123
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Regulator of Ty1 transposition protein 102
C, F
158Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RTT102
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53330
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 79.387α = 109.03
b = 87.982β = 104.64
c = 105.430γ = 96.20
Software Package:
Software NamePurpose
SAINTdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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