› 5edv

X-ray diffraction
3.48Å resolution

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex

Released:
DOI: 10.2210/pdb5edv/pdb
PDB entry 5edv coloured by chain, front view.
PDB entry 5edv coloured by chain, side view.
PDB entry 5edv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation.
Lechtenberg BC, Rajput A, Sanishvili R, Dobaczewska MK, Ware CF, Mace PD, Riedl SJ
Nature 529 546-50 (2016)
PMID: 26789245

Function and Biology Details

Reactions catalysed: 
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
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:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero octamer
monomeric
PDBe Complex ID:
PDB-CPX-143304 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase RNF31 Chains: A, B
Molecule details ›
Chains: A, B
Length: 380 amino acids
Theoretical weight: 43.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96EP0 (Residues: 696-1072; Coverage: 35%)
Gene names: RNF31, ZIBRA
Sequence domains:
Ubiquitin-conjugating enzyme E2 D2 Chains: C, D, I
Molecule details ›
Chains: C, D, I
Length: 149 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 16 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 104.82Å b: 75.74Å c: 120.96Å
α: 90° β: 95.56° γ: 90°
R-values:
R R work R free
0.251 0.249 0.303
Expression system: Escherichia coli

Quick links

Citations

37 review citations

Ubiquitin modifications.
Swatek et al. (2016)
36 more

26 mentions without citation

Structural insights into the catalysis and regulation of E3 ubiquitin ligases.
Buetow et al. (2016)
25 more