4JD2 | pdb_00004jd2

Crystal structure of Bos taurus Arp2/3 complex binding with Mus musculus GMF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 
    0.248 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

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This is version 1.4 of the entry. See complete history


Literature

Structural basis for regulation of Arp2/3 complex by GMF.

Luan, Q.Nolen, B.J.

(2013) Nat Struct Mol Biol 20: 1062-1068

  • DOI: https://doi.org/10.1038/nsmb.2628
  • Primary Citation of Related Structures:  
    4JD2

  • PubMed Abstract: 

    The Arp2/3 complex mediates formation of complex cellular structures such as lamellipodia by nucleating branched actin filaments. Arp2/3-complex activity is precisely controlled by over a dozen regulators, yet the structural mechanism by which regulators interact with the complex is unknown. GMF is a recently discovered regulator of the Arp2/3 complex that can inhibit nucleation and disassemble branches. We solved the structure of the 240-kDa assembly of Mus musculus GMF and Bos taurus Arp2/3 complex and found that GMF binds the barbed end of Arp2, overlapping with the proposed binding site of WASP-family proteins. The structure suggests that GMF can bind branch junctions in the manner that cofilin binds filament sides, consistent with a modified cofilin-like mechanism for debranching by GMF. The GMF-Arp2 interface reveals how the ADF-H actin-binding domain in GMF is exploited to specifically recognize Arp2/3 complex and not actin.


  • Organizational Affiliation

    1] Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA. [2] Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
UniProt
Find proteins for P61157 (Bos taurus)
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UniProt GroupP61157
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
UniProt
Find proteins for A7MB62 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
UniProt
Find proteins for Q58CQ2 (Bos taurus)
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UniProt GroupQ58CQ2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3MHR7 (Bos taurus)
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UniProt GroupQ3MHR7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
UniProt
Find proteins for Q148J6 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3SYX9 (Bos taurus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Glia maturation factor gamma142Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ERL7 (Mus musculus)
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IMPC:  MGI:1927135
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free:  0.248 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.538α = 90
b = 231.538β = 90
c = 109.743γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2013-08-14
    Changes: Database references
  • Version 1.3: 2013-09-18
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations