› 3k9p

X-ray diffraction
2.8Å resolution

The crystal structure of E2-25K and ubiquitin complex

Released:
DOI: 10.2210/pdb3k9p/pdb
PDB entry 3k9p coloured by chain, front view.
PDB entry 3k9p coloured by chain, side view.
PDB entry 3k9p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity.
Ko S, Kang GB, Song SM, Lee JG, Shin DY, Yun JH, Sheng Y, Cheong C, Jeon YH, Jung YK, Arrowsmith CH, Avvakumov GV, Dhe-Paganon S, Yoo YJ, Eom SH, Lee W
J Biol Chem 285 36070-80 (2010)
PMID: 20826778

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

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-143362 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 K Chain: A
Molecule details ›
Chain: A
Length: 217 amino acids
Theoretical weight: 24.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61086 (Residues: 1-200; Coverage: 100%)
Gene names: HIP2, LIG, UBE2K
Sequence domains:
Structure domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 79 amino acids
Theoretical weight: 8.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P21
Unit cell:
a: 43.554Å b: 50.974Å c: 63.906Å
α: 90° β: 102.62° γ: 90°
R-values:
R R work R free
0.282 0.232 0.296
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Oxidative stress, neurodegeneration, and the balance of protein degradation and protein synthesis.
Dasuri et al. (2013)
8 more

6 mentions without citation

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