› 3eb6

X-ray diffraction
3.4Å resolution

Structure of the cIAP2 RING domain bound to UbcH5b

Released:
DOI: 10.2210/pdb3eb6/pdb
PDB entry 3eb6 coloured by chain, front view.
PDB entry 3eb6 coloured by chain, side view.
PDB entry 3eb6 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the cIAP2 RING domain reveal conformational changes associated with ubiquitin-conjugating enzyme (E2) recruitment.
Mace PD, Linke K, Feltham R, Schumacher FR, Smith CA, Vaux DL, Silke J, Day CL
J Biol Chem 283 31633-40 (2008)
PMID: 18784070

Function and Biology Details

Reactions 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
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158737 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Baculoviral IAP repeat-containing protein 3 Chain: A
Molecule details ›
Chain: A
Length: 74 amino acids
Theoretical weight: 8.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13489 (Residues: 536-604; Coverage: 11%)
Gene names: API2, BIRC3, MIHC, RNF49
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin-conjugating enzyme E2 D2 Chain: B
Molecule details ›
Chain: B
Length: 149 amino acids
Theoretical weight: 16.9 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62840 (Residues: 1-147; Coverage: 100%)
Gene names: ubc4, ube2d2, ube2d3.1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P6322
Unit cell:
a: 137.226Å b: 137.226Å c: 111.87Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.283 0.281 0.32
Expression system: Escherichia coli

Quick links

Citations

31 review citations

RING domain E3 ubiquitin ligases.
Deshaies et al. (2009)
30 more

21 mentions without citation

Molecular cell death platforms and assemblies.
Mace et al. (2010)
20 more