› 5aiu

X-ray diffraction
2.21Å resolution

A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)

Released:
DOI: 10.2210/pdb5aiu/pdb
PDB entry 5aiu coloured by chain, front view.
PDB entry 5aiu coloured by chain, side view.
PDB entry 5aiu coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains.
Branigan E, Plechanovová A, Jaffray EG, Naismith JH, Hay RT
Nat Struct Mol Biol 22 597-602 (2015)
PMID: 26148049

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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-131589 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase RNF4 Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 14.76 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O88846 (Residues: 131-194; Coverage: 33%)
Gene names: Rnf4, Snurf
Sequence domains: Ring finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin-conjugating enzyme E2 N Chains: B, E
Molecule details ›
Chains: B, E
Length: 154 amino acids
Theoretical weight: 17.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21212
Unit cell:
a: 69.19Å b: 169.21Å c: 52.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.217 0.255
Expression system: Escherichia coli

Quick links

Citations

20 review citations

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

6 mentions without citation

Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains.
Branigan et al. (2015)
5 more