2IBF

Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Vinculin binding in its closed conformation by a helix addition mechanism.

Nhieu, G.T.Izard, T.

(2007) EMBO J 26: 4588-4596

  • DOI: 10.1038/sj.emboj.7601863
  • Primary Citation of Related Structures:  
    2IBF

  • PubMed Abstract: 
  • Vinculin links integrin receptors to the actin cytoskeleton by binding to talin. Vinculin is held in an inactive, closed-clamp conformation through hydrophobic interactions between its head and tail domains, and vinculin activation has long been thought to be dependent upon severing the head-tail interaction ...

    Vinculin links integrin receptors to the actin cytoskeleton by binding to talin. Vinculin is held in an inactive, closed-clamp conformation through hydrophobic interactions between its head and tail domains, and vinculin activation has long been thought to be dependent upon severing the head-tail interaction. Talin, alpha-actinin, and the invasin IpaA of Shigella flexneri sever vinculin's head-tail interaction by inserting an alpha-helix into vinculin's N-terminal four-helical bundle, provoking extensive conformational changes by a helical bundle conversion mechanism; these alterations in vinculin structure displace its tail domain, allowing vinculin to bind to its other partners. IpaA harbors two juxtaposed alpha-helical vinculin-binding sites (VBS) in its C-terminus. Here, we report that the lower affinity VBS of IpaA can also bind to the adjacent C-terminal four-helical bundle of vinculin's head domain through a helix addition mechanism. These hydrophobic interactions do not alter the conformation of this helical bundle, and the architecture of the complex suggests that IpaA can simultaneously interact with both of the four-helical bundle domains of vinculin's N-terminus to stabilize vinculin-IpaA interactions.


    Organizational Affiliation

    Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Inserm U786, Paris, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VinculinA266Homo sapiensMutation(s): 0 
Gene Names: VCL
UniProt & NIH Common Fund Data Resources
Find proteins for P18206 (Homo sapiens)
Explore P18206 
Go to UniProtKB:  P18206
PHAROS:  P18206
GTEx:  ENSG00000035403 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18206
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Invasin ipaAB,
C [auth D]
25Shigella flexneriMutation(s): 0 
Gene Names: ipaACP0125
UniProt
Find proteins for P18010 (Shigella flexneri)
Explore P18010 
Go to UniProtKB:  P18010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18010
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.478α = 90
b = 154.478β = 90
c = 154.478γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-09-11 
  • Released Date: 2007-09-18 
  • Deposition Author(s): Izard, T.

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance