3DWL

Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.78 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.324 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and biochemical properties of fission yeast arp2/3 complex lacking the arp2 subunit.

Nolen, B.J.Pollard, T.D.

(2008) J.Biol.Chem. 283: 26490-26498

  • DOI: 10.1074/jbc.M802607200

  • PubMed Abstract: 
  • Arp2/3 (actin-related protein 2/3) complex is a seven-subunit complex that nucleates branched actin filaments in response to cellular signals. Nucleation-promoting factors such as WASp/Scar family proteins activate the complex by facilitating the act ...

    Arp2/3 (actin-related protein 2/3) complex is a seven-subunit complex that nucleates branched actin filaments in response to cellular signals. Nucleation-promoting factors such as WASp/Scar family proteins activate the complex by facilitating the activating conformational change and recruiting the first actin monomer for the daughter branch. Here we address the role of the Arp2 subunit in the function of Arp2/3 complex by isolating a version of the complex lacking Arp2 (Arp2Delta Arp2/3 complex) from fission yeast. An x-ray crystal structure of the DeltaArp2 Arp2/3 complex showed that the rest of the complex is unperturbed by the loss of Arp2. However, the Arp2Delta Arp2/3 complex was inactive in actin nucleation assays, indicating that Arp2 is essential to form a branch. A fluorescence anisotropy assay showed that Arp2 does not contribute to the affinity of the complex for Wsp1-VCA, a Schizosaccharomyces pombe nucleation-promoting factor protein. Fluorescence resonance energy transfer experiments showed that the loss of Arp2 does not prevent VCA from recruiting an actin monomer to the complex. Truncation of the N terminus of ARPC5, the smallest subunit in the complex, increased the yield of Arp2Delta Arp2/3 complex during purification but did not compromise nucleation activity of the full Arp2/3 complex.


    Organizational Affiliation

    Departments of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA. bradley.nolen@yale.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 3
A, B
427Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: act2
Find proteins for P32390 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P32390
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 1
C, H
377Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: arc1 (sop2)
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P78774
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 2
D, I
317Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: arc2 (arc34)
Find proteins for O14241 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14241
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 3
E, J
174Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: arc3 (arc21)
Find proteins for Q9Y7J4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y7J4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 4
F, K
168Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: arc4 (arp20)
Find proteins for Q92352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q92352
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 5
G, L
152Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: arc5 (arc16)
Find proteins for Q10316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10316
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.78 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.324 
  • Space Group: P 42 2 2
Unit Cell:
Length (Å)Angle (°)
a = 218.967α = 90.00
b = 218.967β = 90.00
c = 315.049γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance