› 6w7z

X-ray diffraction
1.8Å resolution

RNF12 RING domain in complex with Ube2d2

Released:
DOI: 10.2210/pdb6w7z/pdb
Model geometry
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PDB entry 6w7z coloured by chain, front view.
PDB entry 6w7z coloured by chain, side view.
PDB entry 6w7z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains.
Middleton AJ, Zhu J, Day CL
J Mol Biol 432 3790-3801 (2020)
PMID: 32416094

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-158734 (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: 17.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
  • Best match: P62837-2 (Residues: 1-118)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
E3 ubiquitin-protein ligase RLIM Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NVW2 (Residues: 530-624; Coverage: 15%)
Gene names: RLIM, RNF12
Sequence domains: Ring finger domain

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand ZN 2 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: P21
Unit cell:
a: 48.441Å b: 50.453Å c: 54.375Å
α: 90° β: 99.72° γ: 90°
R-values:
R R work R free
0.18 0.178 0.211
Expression system: Escherichia coli

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Citations

1 review citation

Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road.
Lacoursiere et al. (2022)
5 other articles

2 mentions without citation

Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation.
Márquez-Cantudo et al. (2021)
1 more

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