PDBe 4whv

X-ray diffraction
8.3Å resolution

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B

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. 
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: A, F, G, L
Molecule details ›
Chains: A, F, G, L
Length: 83 amino acids
Theoretical weight: 9.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase RNF8 Chains: C, D, I, J
Molecule details ›
Chains: C, D, I, J
Length: 149 amino acids
Theoretical weight: 17.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O76064 (Residues: 345-485; Coverage: 29%)
Gene names: KIAA0646, RNF8
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Ubiquitin-conjugating enzyme E2 N Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 160 amino acids
Theoretical weight: 17.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P6422
Unit cell:
a: 341.379Å b: 341.379Å c: 113.447Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.33 0.329 0.337
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)