› 6c16

X-ray diffraction
3.27Å resolution

Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.

Released:
DOI: 10.2210/pdb6c16/pdb
PDB entry 6c16 coloured by chain, front view.
PDB entry 6c16 coloured by chain, side view.
PDB entry 6c16 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)
PDBe Complex ID:
PDB-CPX-143263 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
S-phase kinase-associated protein 1 Chains: A, B
Molecule details ›
Chains: A, B
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 2A Chains: C, F
Molecule details ›
Chains: C, F
Length: 47 amino acids
Theoretical weight: 5.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2K7 (Residues: 888-932; Coverage: 4%)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Sequence domains: F-box domain
Ubiquitin Chains: D, H
Molecule details ›
Chains: D, H
Length: 86 amino acids
Theoretical weight: 9.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-163, 164-228; 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: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 38.241Å b: 119.582Å c: 63.707Å
α: 90° β: 98.45° γ: 90°
R-values:
R R work R free
0.263 0.26 0.317
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

1 mention without citation

A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
Gorelik et al. (2018)