› 3ckd

X-ray diffraction
2.65Å resolution

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

Released:
DOI: 10.2210/pdb3ckd/pdb
PDB entry 3ckd coloured by chain, front view.
PDB entry 3ckd coloured by chain, side view.
PDB entry 3ckd coloured by chain, top view.
Source organism: Shigella flexneri 2a str. 301
Primary publication:
Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.
Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A
Nat Struct Mol Biol 15 1293-301 (2008)
PMID: 18997778

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148257 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase ipaH7.8 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 312 amino acids
Theoretical weight: 35.64 KDa
Source organism: Shigella flexneri 2a str. 301
Expression system: Escherichia coli
UniProt:
  • Canonical: P18014 (Residues: 255-273, 274-560; Coverage: 54%)
Gene names: CP0078, SFLP133, ipaH7.8, pWR501_0084
Sequence domains: C-terminal novel E3 ligase, LRR-interacting
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand GOL 3 x GOL
Ligand PEG 1 x PEG
1 modified residue:
Ligand MSE 21 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I422
Unit cell:
a: 128.928Å b: 128.928Å c: 282.825Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.228 0.284
Expression system: Escherichia coli

Quick links

Citations

43 review citations

Common themes in the design and function of bacterial effectors.
Galán JE. (2009)
42 more

7 mentions without citation

Hijacking the host ubiquitin pathway: structural strategies of bacterial E3 ubiquitin ligases.
Hicks et al. (2010)
6 more