› 4f8c

X-ray diffraction
1.95Å resolution

Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8

Released:
DOI: 10.2210/pdb4f8c/pdb
PDB entry 4f8c coloured by chain, front view.
PDB entry 4f8c coloured by chain, side view.
PDB entry 4f8c coloured by chain, top view.
Source organisms:
Primary publication:
The molecular basis of Nedd8 deamidation by the bacterial effector protein Cif
Crow A, Hughes RK, Taieb F, Oswald E, Banfield MJ
Proc. Natl. Acad. Sci. U.S.A. (2012)

Function and Biology Details

Reaction catalysed: 
Protein L-glutamine + H(2)O = protein L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101803 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein-glutamine deamidase Cif Chains: A, C
Molecule details ›
Chains: A, C
Length: 275 amino acids
Theoretical weight: 30.81 KDa
Source organism: Yersinia pseudotuberculosis YPIII
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H3B1Q8 (Residues: 33-288; Coverage: 88%)
Gene names: YPK_1971, cif
Sequence domains: Cycle inhibiting factor (CIF)
NEDD8 Chains: B, D
Molecule details ›
Chains: B, D
Length: 88 amino acids
Theoretical weight: 10.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-81; Coverage: 100%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P6322
Unit cell:
a: 125.359Å b: 125.359Å c: 169.93Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.187 0.235
Expression system: Escherichia coli

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