2P9U

Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Insights into the Influence of Nucleotides on Actin Family Proteins from Seven Structures of Arp2/3 Complex.

Nolen, B.J.Pollard, T.D.

(2007) Mol Cell 26: 449-457

  • DOI: https://doi.org/10.1016/j.molcel.2007.04.017
  • Primary Citation of Related Structures:  
    2P9I, 2P9K, 2P9L, 2P9N, 2P9P, 2P9S, 2P9U

  • PubMed Abstract: 

    ATP is required for nucleation of actin filament branches by Arp2/3 complex, but the influence of ATP binding and hydrolysis are poorly understood. We determined crystal structures of bovine Arp2/3 complex cocrystallized with various bound adenine nucleotides and cations. Nucleotide binding favors closure of the nucleotide-binding cleft of Arp3, but no large-scale conformational changes in the complex. Thus, ATP binding does not directly activate Arp2/3 complex but is part of a network of interactions that contribute to nucleation. We compared nucleotide-induced conformational changes of residues lining the cleft in Arp3 and actin structures to construct a movie depicting the proposed ATPase cycle for the actin family. Chemical crosslinking stabilized subdomain 1 of Arp2, revealing new electron density for 69 residues in this subdomain. Steric clashes with Arp3 appear to be responsible for intrinsic disorder of subdomains 1 and 2 of Arp2 in inactive Arp2/3 complex.


  • Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 3418Bos taurusMutation(s): 0 
Gene Names: ACTR3
UniProt
Find proteins for P61157 (Bos taurus)
Explore P61157 
Go to UniProtKB:  P61157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61157
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 2394Bos taurusMutation(s): 0 
Gene Names: ACTR2
UniProt
Find proteins for A7MB62 (Bos taurus)
Explore A7MB62 
Go to UniProtKB:  A7MB62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7MB62
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
UniProt
Find proteins for Q58CQ2 (Bos taurus)
Explore Q58CQ2 
Go to UniProtKB:  Q58CQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58CQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
Gene Names: ARPC2
UniProt
Find proteins for Q3MHR7 (Bos taurus)
Explore Q3MHR7 
Go to UniProtKB:  Q3MHR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3MHR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
Gene Names: ARPC3
UniProt
Find proteins for Q3T035 (Bos taurus)
Explore Q3T035 
Go to UniProtKB:  Q3T035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3T035
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
Gene Names: ARPC4
UniProt
Find proteins for Q148J6 (Bos taurus)
Explore Q148J6 
Go to UniProtKB:  Q148J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ148J6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
Gene Names: ARPC5
UniProt
Find proteins for Q3SYX9 (Bos taurus)
Explore Q3SYX9 
Go to UniProtKB:  Q3SYX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SYX9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.122α = 90
b = 129.355β = 90
c = 203.801γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations