4JHD

Crystal Structure of an Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of actin filament nucleation by tandem w domains.

Chen, X.Ni, F.Tian, X.Kondrashkina, E.Wang, Q.Ma, J.

(2013) Cell Rep 3: 1910-1920

  • DOI: 10.1016/j.celrep.2013.04.028

  • PubMed Abstract: 
  • Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mecha ...

    Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization.


    Organizational Affiliation

    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-5C
A, D
384Drosophila melanogasterMutations: P252K, A213E
Gene Names: Act5C
Find proteins for P10987 (Drosophila melanogaster)
Go to UniProtKB:  P10987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-5C
B, E
384Drosophila melanogasterMutations: P331K, K300E
Gene Names: Act5C
Find proteins for P10987 (Drosophila melanogaster)
Go to UniProtKB:  P10987
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein cordon-bleu
C, F
171Mus musculusGene Names: Cobl (Kiaa0633)
Find proteins for Q5NBX1 (Mus musculus)
Go to UniProtKB:  Q5NBX1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, D, E
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.450α = 65.41
b = 99.800β = 90.03
c = 118.270γ = 77.77
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PHENIXphasing
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references