› 5d0k

X-ray diffraction
2.65Å resolution

Structure of UbE2D2:RNF165:Ub complex

Released:
DOI: 10.2210/pdb5d0k/pdb
PDB entry 5d0k coloured by chain, front view.
PDB entry 5d0k coloured by chain, side view.
PDB entry 5d0k 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 Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 152 amino acids
Theoretical weight: 17.14 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 Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 92 amino acids
Theoretical weight: 10.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ZSG1 (Residues: 255-346; Coverage: 25%)
Gene names: ARK2C, RNF165
Sequence domains: Ring finger domain
Ubiquitin Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
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

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P3
Unit cell:
a: 113.046Å b: 113.046Å c: 135.667Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.238
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 Diversity of Ubiquitin E3 Ligase.
Toma-Fukai et al. (2021)
5 more