› 6d6i

X-ray diffraction
2.55Å resolution

Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13

Released:
DOI: 10.2210/pdb6d6i/pdb
PDB entry 6d6i coloured by chain, front view.
PDB entry 6d6i coloured by chain, side view.
PDB entry 6d6i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes.
Garg P, Ceccarelli DF, Keszei AFA, Kurinov I, Sicheri F, Sidhu SS
J Mol Biol 432 952-966 (2020)
PMID: 31634471

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158210 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 variant 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 143 amino acids
Theoretical weight: 16.14 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13404 (Residues: 8-147; Coverage: 95%)
Gene names: CROC1, P/OKcl.19, UBE2V, UBE2V1, UEV1
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 N Chains: B, E
Molecule details ›
Chains: B, E
Length: 155 amino acids
Theoretical weight: 17.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61088 (Residues: 3-152; Coverage: 99%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin-like domain-containing protein Chains: C, F
Molecule details ›
Chains: C, F
Length: 88 amino acids
Theoretical weight: 10.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96H31 (Residues: 470-545; Coverage: 14%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P32
Unit cell:
a: 91.444Å b: 91.444Å c: 92.446Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.264 0.296
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors.
LaPlante et al. (2021)
4 more

1 mention without citation

Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes.
Garg et al. (2020)