› 4v3l

X-ray diffraction
1.53Å resolution

RNF38-UB-UbcH5B-Ub complex

Released:
DOI: 10.2210/pdb4v3l/pdb
PDB entry 4v3l coloured by chain, front view.
PDB entry 4v3l coloured by chain, side view.
PDB entry 4v3l 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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-143426 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 146 amino acids
Theoretical weight: 16.65 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, D
Molecule details ›
Chains: B, D
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 Chain: C
Molecule details ›
Chain: C
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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3221
Unit cell:
a: 62.84Å b: 62.84Å c: 191.06Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.183 0.193
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

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

14 mentions without citation

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