3CKD | pdb_00003ckd

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 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 107.5 kDa 
  • Atom Count: 6,327 
  • Modeled Residue Count: 778 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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: ipaH1.4, CP0265
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
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

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.284 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.231 (Depositor) 
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

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Entry History 

Deposition Data

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
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary