4ap4

X-ray diffraction
2.21Å resolution

Rnf4 - ubch5a - ubiquitin heterotrimeric complex

Released:

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

Structure analysis Details

Assembly composition:
hetero pentamer (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 D1 Chains: B, E
Molecule details ›
Chains: B, E
Length: 153 amino acids
Theoretical weight: 17.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51668 (Residues: 1-147; Coverage: 100%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 80 amino acids
Theoretical weight: 8.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 608-684; 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:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 50.48Å b: 65.09Å c: 189.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.208 0.242
Expression system: Escherichia coli