› 8gcb

X-ray diffraction
2.39Å resolution

Structure of RNF125 in complex with a UbcH5b~Ub conjugate

Released:
DOI: 10.2210/pdb8gcb/pdb
Model geometry
Fit model/data
PDB entry 8gcb coloured by chain, front view.
PDB entry 8gcb coloured by chain, side view.
PDB entry 8gcb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation.
Middleton AJ, Barzak FM, Fokkens TJ, Nguyen K, Day CL
Structure (2023)
PMID: 37541247

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-274090 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 17.21 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
E3 ubiquitin-protein ligase RNF125 Chain: B
Molecule details ›
Chain: B
Length: 101 amino acids
Theoretical weight: 11.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96EQ8 (Residues: 32-127; Coverage: 41%)
Gene name: RNF125
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P43212
Unit cell:
a: 59.325Å b: 59.325Å c: 185.821Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.254 0.253 0.271
Expression system: Escherichia coli

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