› 5dka

X-ray diffraction
1.55Å resolution

A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125

Released:
DOI: 10.2210/pdb5dka/pdb
PDB entry 5dka coloured by chain, front view.
PDB entry 5dka coloured by chain, side view.
PDB entry 5dka coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.
Bijlmakers MJ, Teixeira JM, Boer R, Mayzel M, Puig-Sàrries P, Karlsson G, Coll M, Pons M, Crosas B
Sci Rep 6 29232 (2016)
PMID: 27411375

Function and Biology Details

Reaction 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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188475 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase RNF125 Chains: A, B
Molecule details ›
Chains: A, B
Length: 232 amino acids
Theoretical weight: 26.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96EQ8 (Residues: 1-232; Coverage: 100%)
Gene name: RNF125
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand CL 4 x CL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P212121
Unit cell:
a: 51.67Å b: 52.32Å c: 73.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.239
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
7 other articles

2 mentions without citation

The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1.
Middleton et al. (2017)
1 more