1U2V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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 U S A 101: 15627-15632

  • DOI: 10.1073/pnas.0407149101
  • Primary Citation of Related Structures:  
    1U2V, 1TYQ

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-Related Protein 3A418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-Related Protein 2B394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Arp2/3 Complex 41Kda SubunitC372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Arp2/3 Complex 34Kda SubunitD300Bos taurusMutation(s): 0 
Gene Names: ARPC2
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Arp2/3 Complex 21Kda SubunitE178Bos taurusMutation(s): 0 
Gene Names: ARPC3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Arp2/3 Complex 20Kda SubunitF168Bos taurusMutation(s): 0 
Gene Names: ARPC4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Arp2/3 Complex 16kDa SubunitG151Bos taurusMutation(s): 0 
Gene Names: ARPC5
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.3α = 90
b = 129.3β = 90
c = 204.7γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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