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 
  • R-Value Observed: 0.325 

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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: https://doi.org/10.1074/jbc.M802607200
  • Primary Citation of Related Structures:  
    3DWL

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3A,
G [auth B]		427Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P32390 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP32390
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B [auth C],
H		377Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2C [auth D],
I		317Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14241 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3D [auth E],
J		174Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9Y7J4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4E [auth F],
K		168Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q92352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5F [auth G],
L		152Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
M [auth A],
N [auth B]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.78 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.324 
  • R-Value Observed: 0.325 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.967α = 90
b = 218.967β = 90
c = 315.049γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description