› 5eya

X-ray diffraction
2.4Å resolution

TRIM25 RING domain in complex with Ubc13-Ub conjugate

Released:
DOI: 10.2210/pdb5eya/pdb
PDB entry 5eya coloured by chain, front view.
PDB entry 5eya coloured by chain, side view.
PDB entry 5eya coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.
Sanchez JG, Chiang JJ, Sparrer KMJ, Alam SL, Chi M, Roganowicz MD, Sankaran B, Gack MU, Pornillos O
Cell Rep 16 1315-1325 (2016)
PMID: 27425606

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
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
ATP + [ISG15] + [protein]-lysine = AMP + diphosphate + [protein]-N-ISGyllysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143300 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 N Chains: A, B
Molecule details ›
Chains: A, B
Length: 152 amino acids
Theoretical weight: 17.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
E3 ubiquitin/ISG15 ligase TRIM25 Chains: F, G
Molecule details ›
Chains: F, G
Length: 86 amino acids
Theoretical weight: 9.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q14258 (Residues: 1-83; Coverage: 13%)
Gene names: EFP, RNF147, TRIM25, ZNF147
Sequence domains: RING-type zinc-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
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 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 53.047Å b: 75.779Å c: 169.101Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.189 0.228
Expression system: Escherichia coli

Quick links

Citations

24 review citations

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
23 more

8 mentions without citation

Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases.
Fiorentini et al. (2020)
7 more