1TYQ

Crystal structure of Arp2/3 complex with bound ATP and calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP

Nolen, B.J.Littlefield, R.S.Pollard, T.D.

(2004) Proc.Natl.Acad.Sci.Usa 101: 15627-15632

  • DOI: 10.1073/pnas.0407149101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Actin-related protein (Arp) 2/3 complex stimulates formation of actin filaments at the leading edge of motile cells. Nucleation of filaments depends on hydrolysis of ATP bound to Arp2. Here we report crystal structures of Arp2/3 complex with bound AT ...

    Actin-related protein (Arp) 2/3 complex stimulates formation of actin filaments at the leading edge of motile cells. Nucleation of filaments depends on hydrolysis of ATP bound to Arp2. Here we report crystal structures of Arp2/3 complex with bound ATP or ADP. The nucleotides are immobilized on the face of subdomains 3 and 4 of Arp2, whereas subdomains 1 and 2 are flexible and absent from the electron density maps. This flexibility may explain why Arp2 does not hydrolyze ATP until the complex is activated. ATP stabilizes a relatively closed conformation of Arp3 with the gamma-phosphate bridging loops from opposite sides of the cleft. ADP binds Arp3 in a unique conformation that favors an open cleft, revealing a conformational change that may occur in actin and Arps when ATP is hydrolyzed and phosphate dissociates. These structures provide the an opportunity to compare all nucleotide-binding states in an actin-related protein and give insights into the function of both the Arp2/3 complex and actin.


    Organizational Affiliation

    Departments of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related 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-related 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
Arp2/3 complex 41kDa subunit
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
Arp2/3 complex 34kDa subunit
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
Arp2/3 complex 21kDa subunit
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
Arp2/3 complex 20kDa subunit
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
Arp2/3 Complex 16kDa Subunit
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
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 111.368α = 90.00
b = 129.392β = 90.00
c = 199.692γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance