7zj3

X-ray diffraction
2.53Å resolution

Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate

Released:
Model geometry
Fit model/data

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
(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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-272711 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Tripartite motif-containing protein 2 Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 97 amino acids
Theoretical weight: 10.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9C040 (Residues: 2-95; Coverage: 13%)
Gene names: KIAA0517, RNF86, TRIM2
Sequence domains: RING-type zinc-finger
Ubiquitin-conjugating enzyme E2 D1 Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 150 amino acids
Theoretical weight: 16.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51668 (Residues: 2-146; Coverage: 99%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: C, F, I, L

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 57.319Å b: 123.662Å c: 112.471Å
α: 90° β: 102.803° γ: 90°
R-values:
R R work R free
0.213 0.21 0.258
Expression system: Escherichia coli