3RSE

Structural and biochemical characterization of two binding sites for nucleation promoting factor WASp-VCA on Arp2/3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical characterization of two binding sites for nucleation-promoting factor WASp-VCA on Arp2/3 complex.

Ti, S.C.Jurgenson, C.T.Nolen, B.J.Pollard, T.D.

(2011) Proc Natl Acad Sci U S A 108: E463-E471

  • DOI: 10.1073/pnas.1100125108
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Actin-related protein (Arp) 2/3 complex mediates the formation of actin filament branches during endocytosis and at the leading edge of motile cells. The pathway of branch formation is ambiguous owing to uncertainty regarding the stoichiometry and lo ...

    Actin-related protein (Arp) 2/3 complex mediates the formation of actin filament branches during endocytosis and at the leading edge of motile cells. The pathway of branch formation is ambiguous owing to uncertainty regarding the stoichiometry and location of VCA binding sites on Arp2/3 complex. Isothermal titration calorimetry showed that the CA motif from the C terminus of fission yeast WASP (Wsp1p) bound to fission yeast and bovine Arp2/3 complex with a stoichiometry of 2 to 1 and very different affinities for the two sites (K(d)s of 0.13 and 1.6 μM for fission yeast Arp2/3 complex). Equilibrium binding, kinetic, and cross-linking experiments showed that (i) CA at high-affinity site 1 inhibited Arp2/3 complex binding to actin filaments, (ii) low-affinity site 2 had a higher affinity for CA when Arp2/3 complex was bound to actin filaments, and (iii) Arp2/3 complex had a much higher affinity for free CA than VCA cross-linked to an actin monomer. Crystal structures showed the C terminus of CA bound to the low-affinity site 2 on Arp3 of bovine Arp2/3 complex. The C helix is likely to bind to the barbed end groove of Arp3 in a position for VCA to deliver the first actin subunit to the daughter filament.


    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 LengthOrganismDetails
Actin-related protein 3
A
418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
Find proteins for P61157 (Bos taurus)
Go to UniProtKB:  P61157
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2
B
394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
Find proteins for A7MB62 (Bos taurus)
Go to UniProtKB:  A7MB62
Protein Feature View
  • Reference Sequence

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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 UniProtKB:  Q58CQ2
Protein Feature View
  • Reference Sequence

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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 UniProtKB:  Q3MHR7
Protein Feature View
  • Reference Sequence

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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 UniProtKB:  Q3T035
Protein Feature View
  • Reference Sequence

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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 UniProtKB:  Q148J6
Protein Feature View
  • Reference Sequence

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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 UniProtKB:  Q3SYX9
Protein Feature View
  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CA fragment of Bos taurus N-WASP
Z
3Bos taurusMutation(s): 0 
Gene Names: WASL
Find proteins for Q95107 (Bos taurus)
Go to UniProtKB:  Q95107
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.443α = 90
b = 129.34β = 90
c = 204.559γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-14
    Changes: Database references