› 5d0m

X-ray diffraction
1.91Å resolution

Structure of UbE2D2:RNF165:Ub complex

Released:
DOI: 10.2210/pdb5d0m/pdb
PDB entry 5d0m coloured by chain, front view.
PDB entry 5d0m coloured by chain, side view.
PDB entry 5d0m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.
Wright JD, Mace PD, Day CL
Nat Struct Mol Biol 23 45-52 (2016)
PMID: 26656854

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-143260 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 17.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
E3 ubiquitin-protein ligase ARK2C Chain: C
Molecule details ›
Chain: C
Length: 87 amino acids
Theoretical weight: 9.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ZSG1 (Residues: 255-346; Coverage: 24%)
Gene names: ARK2C, RNF165
Sequence domains: Ring finger domain
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P43
Unit cell:
a: 62.62Å b: 62.62Å c: 82.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.179 0.213
Expression system: Escherichia coli

Quick links

Citations

11 review citations

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

6 mentions without citation

Structural basis of generic versus specific E2-RING E3 interactions in protein ubiquitination.
Gundogdu et al. (2019)
5 more