4I6M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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 U S A 110: 3345-3350

  • DOI: 10.1073/pnas.1215379110
  • Primary Citation of Related Structures:  
    4I6M

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 7A477Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12406
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UniProt GroupQ12406
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP9B439Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP9Arp9/YMR033WSWP59YM9973.07YMR033W
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein ARP9C106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF2SNF2/YOR290CSWI2TYE3YOR290CGAM1HAF1RIC1
EC: 3.6.4
UniProt
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102D157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT102RTT102/YGR275WYGR275WG9378
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53330
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.374α = 90
b = 104.138β = 93.78
c = 81.319γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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