› 5fer

X-ray diffraction
2.34Å resolution

Complex of TRIM25 RING with UbcH5-Ub

Released:
DOI: 10.2210/pdb5fer/pdb
PDB entry 5fer coloured by chain, front view.
PDB entry 5fer coloured by chain, side view.
PDB entry 5fer coloured by chain, top view.
Source organisms:
Primary publication:
Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.
Koliopoulos MG, Esposito D, Christodoulou E, Taylor IA, Rittinger K
EMBO J 35 1204-18 (2016)
PMID: 27154206

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-156393 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin/ISG15 ligase TRIM25 Chains: A, D
Molecule details ›
Chains: A, D
Length: 85 amino acids
Theoretical weight: 9.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q14258 (Residues: 1-82; Coverage: 13%)
Gene names: EFP, RNF147, TRIM25, ZNF147
Sequence domains: RING-type zinc-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin-conjugating enzyme E2 D1 Chains: B, E
Molecule details ›
Chains: B, E
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51668 (Residues: 1-147; Coverage: 100%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P62992 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
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: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 60.48Å b: 71.7Å c: 160.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.227 0.273
Expression system: Escherichia coli

Quick links

Citations

21 review citations

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

17 mentions without citation

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