› 5vzu

X-ray diffraction
2.7Å resolution

Crystal structure of the Skp1-FBXO31-cyclin D1 complex

Released:
DOI: 10.2210/pdb5vzu/pdb
PDB entry 5vzu coloured by chain, front view.
PDB entry 5vzu coloured by chain, side view.
PDB entry 5vzu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCFFBXO31 ubiquitin ligase.
Li Y, Jin K, Bunker E, Zhang X, Luo X, Liu X, Hao B
Proc Natl Acad Sci U S A 115 319-324 (2018)
PMID: 29279382

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-150220 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
S-phase kinase-associated protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 149 amino acids
Theoretical weight: 16.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 91%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Structure domains: Potassium Channel Kv1.1; Chain A
F-box only protein 31 Chains: B, D
Molecule details ›
Chains: B, D
Length: 488 amino acids
Theoretical weight: 55.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5XUX0 (Residues: 66-539; Coverage: 88%)
Gene names: FBX14, FBX31, FBXO31, PP2386
Sequence domains:
G1/S-specific cyclin-D1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 17 amino acids
Theoretical weight: 1.97 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P24385 (Residues: 279-295; Coverage: 6%)
Gene names: BCL1, CCND1, PRAD1

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand PO4 10 x PO4
1 modified residue:
Ligand TPO 2 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2
Unit cell:
a: 87.679Å b: 156.235Å c: 155.522Å
α: 90° β: 104.21° γ: 90°
R-values:
R R work R free
0.183 0.18 0.233
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones.
Ishida et al. (2021)
6 more

11 mentions without citation

Structural insights into the functional diversity of the CDK-cyclin family.
Wood et al. (2018)
10 more