› 6if1

X-ray diffraction
2.47Å resolution

Crystal structure of Ube2K and K48-linked di-ubiquitin complex

Released:
DOI: 10.2210/pdb6if1/pdb
PDB entry 6if1 coloured by chain, front view.
PDB entry 6if1 coloured by chain, side view.
PDB entry 6if1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis.
Lee JG, Youn HS, Kang JY, Park SY, Kidera A, Yoo YJ, Eom SH
Biochem Biophys Res Commun 506 102-107 (2018)
PMID: 30336976

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143254 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 K Chains: A, B
Molecule details ›
Chains: A, B
Length: 199 amino acids
Theoretical weight: 22.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61086 (Residues: 1-199; Coverage: 100%)
Gene names: HIP2, LIG, UBE2K
Sequence domains:
Structure domains:
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P21
Unit cell:
a: 41.559Å b: 38.792Å c: 190.321Å
α: 90° β: 90.1° γ: 90°
R-values:
R R work R free
0.216 0.215 0.236
Expression system: Escherichia coli

Quick links

Citations

1 review citation

From seeds to trees: how E2 enzymes grow ubiquitin chains.
Middleton et al. (2023)
4 other articles

5 mentions without citation

Huntingtin Ubiquitination Mechanisms and Novel Possible Therapies to Decrease the Toxic Effects of Mutated Huntingtin.
Fiorillo et al. (2021)
4 more