2P9I

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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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:  
    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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein 3A418Bos taurusMutation(s): 0 
Gene Names: ACTR3, ARP3
UniProt
Find proteins for P61157 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-like protein 2B394Bos taurusMutation(s): 0 
Gene Names: ACTR2, ARP2
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BC372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
UniProt
Find proteins for Q58CQ2 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2D300Bos taurusMutation(s): 0 
Gene Names: ARPC2
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3E178Bos taurusMutation(s): 0 
Gene Names: ARPC3
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4F168Bos taurusMutation(s): 0 
Gene Names: ARPC4
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5G151Bos taurusMutation(s): 0 
Gene Names: ARPC5
UniProt
Find proteins for Q3SYX9 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP
Download Ideal Coordinates CCD File 
I [auth A], K [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
H [auth A], J [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.61α = 90
b = 128.184β = 90
c = 198.295γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
CNSphasing

Structure Validation

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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