› 6bva

X-ray diffraction
2.66Å resolution

Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex.

Released:
DOI: 10.2210/pdb6bva/pdb
PDB entry 6bva coloured by chain, front view.
PDB entry 6bva coloured by chain, side view.
PDB entry 6bva coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
Gorelik M, Manczyk N, Pavlenco A, Kurinov I, Sidhu SS, Sicheri F
Structure 26 1226-1236.e3 (2018)
PMID: 30033217

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
S-phase kinase-associated protein 1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 165 amino acids
Theoretical weight: 18.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 100%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Lysine-specific demethylase 2B Chains: E, F
Molecule details ›
Chains: E, F
Length: 47 amino acids
Theoretical weight: 5.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NHM5 (Residues: 1060-1104; Coverage: 3%)
Gene names: CXXC2, FBL10, FBXL10, JHDM1B, KDM2B, NDY1, PCCX2
Sequence domains: F-box-like
Ubiquitin Chains: A, B
Molecule details ›
Chains: A, B
Length: 86 amino acids
Theoretical weight: 9.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 152-163, 164-228; Coverage: 34%)
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: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 65.36Å b: 81.793Å c: 128.685Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.263
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond.
Zhao et al. (2020)
1 more

2 mentions without citation

Emerging drug development technologies targeting ubiquitination for cancer therapeutics.
Veggiani et al. (2019)
1 more