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 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.celrep.2013.04.028
  • Primary Citation of Related Structures:  
    4JHD

  • 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 mechanism of actin nucleation remains poorly understood ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-5C
A, D
384Drosophila melanogasterMutation(s): 2 
Gene Names: Act5CCG4027
UniProt
Find proteins for P10987 (Drosophila melanogaster)
Explore P10987 
Go to UniProtKB:  P10987
Entity Groups  
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UniProt GroupP10987
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-5C
B, E
384Drosophila melanogasterMutation(s): 2 
Gene Names: Act5CCG4027
UniProt
Find proteins for P10987 (Drosophila melanogaster)
Explore P10987 
Go to UniProtKB:  P10987
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UniProt GroupP10987
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cordon-bleu
C, F
171Mus musculusMutation(s): 0 
Gene Names: CoblKiaa0633
UniProt
Find proteins for Q5NBX1 (Mus musculus)
Explore Q5NBX1 
Go to UniProtKB:  Q5NBX1
Entity Groups  
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UniProt GroupQ5NBX1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.45α = 65.41
b = 99.8β = 90.03
c = 118.27γ = 77.77
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description