2P9S

Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.molcel.2007.04.017
  • Primary Citation of Related Structures:  

  • 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 nu ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein 3
A
418Bos taurusMutation(s): 0 
Gene Names: ACTR3 (ARP3)
Find proteins for P61157 (Bos taurus)
Go to Gene View: ACTR3
Go to UniProtKB:  P61157
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein 2
B
394Bos taurusMutation(s): 0 
Gene Names: ACTR2 (ARP2)
Find proteins for A7MB62 (Bos taurus)
Go to Gene View: ACTR2
Go to UniProtKB:  A7MB62
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 1B
C
372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus)
Go to Gene View: ARPC1B
Go to UniProtKB:  Q58CQ2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 2
D
300Bos taurusMutation(s): 0 
Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus)
Go to Gene View: ARPC2
Go to UniProtKB:  Q3MHR7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 3
E
178Bos taurusMutation(s): 0 
Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus)
Go to Gene View: ARPC3
Go to UniProtKB:  Q3T035
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 4
F
168Bos taurusMutation(s): 0 
Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus)
Go to Gene View: ARPC4
Go to UniProtKB:  Q148J6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 5
G
151Bos taurusMutation(s): 0 
Gene Names: ARPC5
Find proteins for Q3SYX9 (Bos taurus)
Go to Gene View: ARPC5
Go to UniProtKB:  Q3SYX9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 111.020α = 90.00
b = 128.694β = 90.00
c = 201.402γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
CNSrefinement
CBASSdata collection
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance