5VZT

Crystal structure of the Skp1-FBXO31 complex

  • Classification: CELL CYCLE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2017-05-29 Released: 2018-01-17 
  • Deposition Author(s): Li, Y., Jin, K., Hao, B.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Connecticut Regenerative Medicine Research Fund 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 319-324

  • DOI: 10.1073/pnas.1708677115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumor cell proliferation and survival. The SCF <sup>FBXO31 </sup> (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation. Pre ...

    Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumor cell proliferation and survival. The SCF FBXO31 (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation. Previous studies have suggested that cyclin D1 levels are maintained at steady state by phosphorylation-dependent nuclear export and subsequent proteolysis in the cytoplasm. Here we present the crystal structures of the Skp1-FBXO31 complex alone and bound to a phosphorylated cyclin D1 C-terminal peptide. FBXO31 possesses a unique substrate-binding domain consisting of two β-barrel motifs, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 β-barrel. Biophysical and functional studies demonstrate that SCF FBXO31 is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner. Our findings provide a conceptual framework for understanding the substrate specificity of the F-box protein FBXO31 and the mechanism of FBXO31-regulated cyclin D1 protein turnover.


    Organizational Affiliation

    Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030; bhao@uchc.edu.,Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030.,Biomolecular Resource Facility, University of Texas Medical Branch, Galveston, TX 77555.,Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1
A, C
149Homo sapiensMutation(s): 1 
Gene Names: SKP1 (EMC19, OCP2, SKP1A, TCEB1L)
Find proteins for P63208 (Homo sapiens)
Go to Gene View: SKP1
Go to UniProtKB:  P63208
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
F-box only protein 31
B, D
488Homo sapiensMutation(s): 0 
Gene Names: FBXO31 (FBX14, FBX31)
Find proteins for Q5XUX0 (Homo sapiens)
Go to Gene View: FBXO31
Go to UniProtKB:  Q5XUX0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
B, D
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.521α = 90.00
b = 156.310β = 103.62
c = 154.596γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-29 
  • Released Date: 2018-01-17 
  • Deposition Author(s): Li, Y., Jin, K., Hao, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM099948
Connecticut Regenerative Medicine Research FundUnited States15-RMA-UCHC-04

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release