› 5d1k

X-ray diffraction
1.78Å resolution

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7

Released:
DOI: 10.2210/pdb5d1k/pdb
PDB entry 5d1k coloured by chain, front view.
PDB entry 5d1k coloured by chain, side view.
PDB entry 5d1k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.
Li S, Liang YH, Mariano J, Metzger MB, Stringer DK, Hristova VA, Li J, Randazzo PA, Tsai YC, Ji X, Weissman AM
J Biol Chem 290 30225-39 (2015)
PMID: 26475854

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-158733 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 147 amino acids
Theoretical weight: 16.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
E3 ubiquitin-protein ligase RNF25 Chain: B
Molecule details ›
Chain: B
Length: 133 amino acids
Theoretical weight: 15.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96BH1 (Residues: 126-258; Coverage: 29%)
Gene name: RNF25
Sequence domains: Ring finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

4 bound ligands:
Ligand EDO 3 x EDO
Ligand PEG 1 x PEG
Ligand OXL 1 x OXL
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2
Unit cell:
a: 105.47Å b: 45.658Å c: 67.954Å
α: 90° β: 118.09° γ: 90°
R-values:
R R work R free
0.171 0.17 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

E2 enzymes: more than just middle men.
Stewart et al. (2016)
7 more

4 mentions without citation

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