› 4auq

X-ray diffraction
2.18Å resolution

Structure of BIRC7-UbcH5b-Ub complex.

Released:
DOI: 10.2210/pdb4auq/pdb
PDB entry 4auq coloured by chain, front view.
PDB entry 4auq coloured by chain, side view.
PDB entry 4auq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
BIRC7-E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer.
Dou H, Buetow L, Sibbet GJ, Cameron K, Huang DT
Nat Struct Mol Biol 19 876-83 (2012)
PMID: 22902369

Function and Biology Details

Reactions catalysed: 
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
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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143428 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 147 amino acids
Theoretical weight: 16.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Baculoviral IAP repeat-containing protein 7 30kDa subunit Chains: B, E
Molecule details ›
Chains: B, E
Length: 62 amino acids
Theoretical weight: 6.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96CA5 (Residues: 239-298; Coverage: 20%)
Gene names: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P43212
Unit cell:
a: 100.64Å b: 100.64Å c: 123.899Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

45 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
44 more

32 mentions without citation

RING-type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination.
Metzger et al. (2014)
31 more