4I6M

Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler.

Schubert, H.L.Wittmeyer, J.Kasten, M.M.Hinata, K.Rawling, D.C.Heroux, A.Cairns, B.R.Hill, C.P.

(2013) Proc.Natl.Acad.Sci.USA 110: 3345-3350

  • DOI: 10.1073/pnas.1215379110

  • PubMed Abstract: 
  • The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expressio ...

    The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT-associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of Ty1 transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin-actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-Å-long helix. The ARP-HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by ∼2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.


    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 7
A
477Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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
439Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ARP9 (SWP59)
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05123
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP9
C
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNF2 (GAM1, RIC1, SWI2, TYE3)
EC: 3.6.4.-
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22082
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Regulator of Ty1 transposition protein 102
D
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RTT102
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53330
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 227.374α = 90.00
b = 104.138β = 93.78
c = 81.319γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CBASSdata collection
HKL-2000data scaling
PHENIXrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Source and taxonomy
  • Version 1.2: 2013-03-06
    Type: Database references
  • Version 1.3: 2013-03-13
    Type: Database references
  • Version 1.4: 2017-08-16
    Type: Data collection, Refinement description, Source and taxonomy