Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - ABCDEFG Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer -A2BCDEF 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 225165.11 
• Atom Count: 13976 
• Residue Count: 1981 
• Unique protein chains: 7

2P9I

Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with gluteraldehyde

• DOI: 10.2210/pdb2P9I/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bos taurus


• Deposited: 2007-03-26 Released: 2007-05-29 
• Deposition Author(s): Nolen, B.J., Pollard, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 

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

• PubMed: 17499050 
• DOI: 10.1016/j.molcel.2007.04.017
• Primary Citation of Related Structures:  
  2P9U, 2P9S, 2P9P, 2P9N, 2P9L, 2P9K


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Actin-like protein 3	A	418	Bos taurus	Mutation(s): 0  Gene Names: ACTR3 (ARP3)
Find proteins for P61157 (Bos taurus) Go to Gene View: ACTR3 Go to UniProtKB:  P61157

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Actin-like protein 2	B	394	Bos taurus	Mutation(s): 0  Gene Names: ACTR2 (ARP2)
Find proteins for A7MB62 (Bos taurus) Go to Gene View: ACTR2 Go to UniProtKB:  A7MB62

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Actin-related protein 2/3 complex subunit 1B	C	372	Bos taurus	Mutation(s): 0  Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus) Go to Gene View: ARPC1B Go to UniProtKB:  Q58CQ2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Actin-related protein 2/3 complex subunit 2	D	300	Bos taurus	Mutation(s): 0  Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus) Go to Gene View: ARPC2 Go to UniProtKB:  Q3MHR7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Actin-related protein 2/3 complex subunit 3	E	178	Bos taurus	Mutation(s): 0  Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus) Go to Gene View: ARPC3 Go to UniProtKB:  Q3T035

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Actin-related protein 2/3 complex subunit 4	F	168	Bos taurus	Mutation(s): 0  Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus) Go to Gene View: ARPC4 Go to UniProtKB:  Q148J6

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Actin-related protein 2/3 complex subunit 5	G	151	Bos taurus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 110.610	α = 90.00
b = 128.184	β = 90.00
c = 198.295	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
ADSC	data collection
HKL-2000	data reduction
CNS	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-26 
• Released Date: 2007-05-29 
• Deposition Author(s): Nolen, B.J., Pollard, T.D.

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
• Version 1.3: 2017-10-18
  Type: Refinement description