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: 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Invasion plasmid antigen, secreted by the Mxi-Spa secretion machineryA, B, C312Shigella flexneri 2a str. 301Mutation(s): 0 
Gene Names: ipaH1.4CP0265
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B], E [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth C], G [auth C], H [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 

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