2GDC

Structure of Vinculin VD1 / IpaA560-633 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural mimicry for vinculin activation by IpaA, a virulence factor of Shigella flexneri.

Hamiaux, C.van Eerde, A.Parsot, C.Broos, J.Dijkstra, B.W.

(2006) Embo Rep. 7: 794-799

  • DOI: 10.1038/sj.embor.7400753

  • PubMed Abstract: 
  • Invasion of epithelial cells by Shigella flexneri is characterized by cytoskeletal rearrangements of the host cell membrane, promoting internalization of the bacterium. The bacterial effector IpaA is injected into the epithelial cell by a type III se ...

    Invasion of epithelial cells by Shigella flexneri is characterized by cytoskeletal rearrangements of the host cell membrane, promoting internalization of the bacterium. The bacterial effector IpaA is injected into the epithelial cell by a type III secretion apparatus and recruits vinculin to regulate actin polymerization at the site of entry. We analysed the complex formed between a carboxy-terminal fragment of IpaA (IpaA(560-633)) and the vinculin D1 domain (VD1), both in crystals and in solution. We present evidence that IpaA(560-633) has two alpha-helical vinculin-binding sites that simultaneously bind two VD1 molecules. The interaction of IpaA(560-633) with VD1 is highly similar to the interaction of the endogenous, eukaryotic proteins talin and alpha-actinin with VD1, showing that Shigella uses a structural mimicry strategy to activate vinculin.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vinculin
A
266Gallus gallusMutation(s): 0 
Gene Names: VCL (VINC1)
Find proteins for P12003 (Gallus gallus)
Go to Gene View: VCL
Go to UniProtKB:  P12003
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Invasin ipaA
B
21Shigella flexneriMutation(s): 0 
Gene Names: ipaA
Find proteins for P18010 (Shigella flexneri)
Go to UniProtKB:  P18010
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.684α = 90.00
b = 68.326β = 90.00
c = 96.521γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance