3CKD

Crystal structure of the C-terminal domain of the Shigella type III effector IpaH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.

Singer, A.U.Rohde, J.R.Lam, R.Skarina, T.Kagan, O.Dileo, R.Chirgadze, N.Y.Cuff, M.E.Joachimiak, A.Tyers, M.Sansonetti, P.J.Parsot, C.Savchenko, A.

(2008) Nat Struct Mol Biol 15: 1293-1301

  • DOI: https://doi.org/10.1038/nsmb.1511
  • Primary Citation of Related Structures:  
    3CKD

  • PubMed Abstract: 

    IpaH proteins are E3 ubiquitin ligases delivered by the type III secretion apparatus into host cells upon infection of humans by the Gram-negative pathogen Shigella flexneri. These proteins comprise a variable leucine-rich repeat-containing N-terminal domain and a conserved C-terminal domain harboring an invariant cysteine residue that is crucial for activity. IpaH homologs are encoded by diverse animal and plant pathogens. Here we demonstrate that the IpaH C-terminal domain carries the catalytic activity for ubiquitin transfer and that the N-terminal domain carries the substrate specificity. The structure of the IpaH C-terminal domain, determined to 2.65-A resolution, represents an all-helical fold bearing no resemblance to previously defined E3 ubiquitin ligases. The conserved and essential cysteine residue lies on a flexible, surface-exposed loop surrounded by conserved acidic residues, two of which are crucial for IpaH activity.


  • Organizational Affiliation

    Ontario Centre for Structural Proteomics, Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario M5G1L5, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
A, B, C
312Shigella flexneri 2a str. 301Mutation(s): 0 
Gene Names: ipaH1.4CP0265
EC: 6.3.2.19
UniProt
Find proteins for P18014 (Shigella flexneri)
Explore P18014 
Go to UniProtKB:  P18014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18014
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.928α = 90
b = 128.928β = 90
c = 282.825γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
EPICS-baseddata collection
datadata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance