› 4v3k

X-ray diffraction
2.04Å resolution

RNF38-UbcH5B-UB complex

Released:
DOI: 10.2210/pdb4v3k/pdb
PDB entry 4v3k coloured by chain, front view.
PDB entry 4v3k coloured by chain, side view.
PDB entry 4v3k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Activation of a primed RING E3-E2-ubiquitin complex by non-covalent ubiquitin.
Buetow L, Gabrielsen M, Anthony NG, Dou H, Patel A, Aitkenhead H, Sibbet GJ, Smith BO, Huang DT
Mol Cell 58 297-310 (2015)
PMID: 25801170

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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-143365 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 146 amino acids
Theoretical weight: 16.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: B, E
Molecule details ›
Chains: B, E
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
E3 ubiquitin-protein ligase RNF38 Chains: C, F
Molecule details ›
Chains: C, F
Length: 79 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H0F5 (Residues: 439-515; Coverage: 15%)
Gene name: RNF38
Sequence domains: Ring finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

3 bound ligands:
Ligand CL 6 x CL
Ligand EDO 5 x EDO
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P41212
Unit cell:
a: 139.62Å b: 139.62Å c: 70.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

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

11 mentions without citation

Specificity and disease in the ubiquitin system.
Chaugule et al. (2016)
10 more