› 5ibk

X-ray diffraction
2.5Å resolution

Skp1-F-box in complex with a ubiquitin variant

Released:
DOI: 10.2210/pdb5ibk/pdb
PDB entry 5ibk coloured by chain, front view.
PDB entry 5ibk coloured by chain, side view.
PDB entry 5ibk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.
Gorelik M, Orlicky S, Sartori MA, Tang X, Marcon E, Kurinov I, Greenblatt JF, Tyers M, Moffat J, Sicheri F, Sidhu SS
Proc Natl Acad Sci U S A 113 3527-32 (2016)
PMID: 26976582

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-143262 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
S-phase kinase-associated protein 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 151 amino acids
Theoretical weight: 16.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63208 (Residues: 1-69, 82-163; Coverage: 89%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Structure domains: Potassium Channel Kv1.1; Chain A
F-box/WD repeat-containing protein 7 Chains: B, E
Molecule details ›
Chains: B, E
Length: 63 amino acids
Theoretical weight: 7.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q969H0 (Residues: 263-323; Coverage: 9%)
Gene names: FBW7, FBX30, FBXW7, SEL10
Sequence domains: F-box-like
Structure domains: Monooxygenase
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 78 amino acids
Theoretical weight: 8.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 151-226; 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: P212121
Unit cell:
a: 63.368Å b: 98.015Å c: 107.704Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

A partnership with the proteasome; the destructive nature of GSK3.
Robertson et al. (2018)
15 more

5 mentions without citation

Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants.
Gorelik et al. (2017)
4 more