5IBK

Skp1-F-box in complex with a ubiquitin variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, M.A.Tang, X.Marcon, E.Kurinov, I.Greenblatt, J.F.Tyers, M.Moffat, J.Sicheri, F.Sidhu, S.S.

(2016) Proc.Natl.Acad.Sci.USA 113: 3527-3532

  • DOI: 10.1073/pnas.1519389113

  • PubMed Abstract: 
  • Skp1-Cul1-F-box (SCF) E3 ligases play key roles in multiple cellular processes through ubiquitination and subsequent degradation of substrate proteins. Although Skp1 and Cul1 are invariant components of all SCF complexes, the 69 different human F-box ...

    Skp1-Cul1-F-box (SCF) E3 ligases play key roles in multiple cellular processes through ubiquitination and subsequent degradation of substrate proteins. Although Skp1 and Cul1 are invariant components of all SCF complexes, the 69 different human F-box proteins are variable substrate binding modules that determine specificity. SCF E3 ligases are activated in many cancers and inhibitors could have therapeutic potential. Here, we used phage display to develop specific ubiquitin-based inhibitors against two F-box proteins, Fbw7 and Fbw11. Unexpectedly, the ubiquitin variants bind at the interface of Skp1 and F-box proteins and inhibit ligase activity by preventing Cul1 binding to the same surface. Using structure-based design and phage display, we modified the initial inhibitors to generate broad-spectrum inhibitors that targeted many SCF ligases, or conversely, a highly specific inhibitor that discriminated between even the close homologs Fbw11 and Fbw1. We propose that most F-box proteins can be targeted by this approach for basic research and for potential cancer therapies.


    Organizational Affiliation

    Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
A, D
151Homo sapiensMutation(s): 0 
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/WD repeat-containing protein 7
B, E
63Homo sapiensMutation(s): 0 
Gene Names: FBXW7 (FBW7, FBX30, SEL10)
Find proteins for Q969H0 (Homo sapiens)
Go to Gene View: FBXW7
Go to UniProtKB:  Q969H0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
F, C
78Homo sapiensMutation(s): 15 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.368α = 90.00
b = 98.015β = 90.00
c = 107.704γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-126129
Canadian Institutes of Health ResearchCanada(MOP-136956
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-13
    Type: Data collection
  • Version 1.2: 2017-09-13
    Type: Advisory, Author supporting evidence, Derived calculations