6C16

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, S.S.Sicheri, F.

(2018) Structure 26: 1226

  • DOI: 10.1016/j.str.2018.06.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Skp1-Cul1-F-box (SCF) E3 ligases constitute the largest and best-characterized family of the multisubunit E3 ligases with important cellular functions and numerous disease links. The specificity of an SCF E3 ligase is established by one of the 69 hum ...

    Skp1-Cul1-F-box (SCF) E3 ligases constitute the largest and best-characterized family of the multisubunit E3 ligases with important cellular functions and numerous disease links. The specificity of an SCF E3 ligase is established by one of the 69 human F-box proteins that are recruited to Cul1 through the Skp1 adaptor. We previously reported generation of ubiquitin variants (UbVs) targeting Fbw7 and Fbw11, which inhibit ligase activity by binding at the F-box-Skp1 interface to competitively displace Cul1. In the present study, we employed an optimized engineering strategy to generate specific binding UbVs against 17 additional Skp1-F-box complexes. We validated our design strategy and uncovered the structural basis of binding specificity by crystallographic analyses of representative UbVs bound to Skp1-Fbl10 and Skp1-Fbl11. Our study highlights the power of combining phage display with structure-based design to develop UbVs targeting specific protein surfaces.


    Organizational Affiliation

    Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sicheri@lunenfeld.ca.,Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA.,Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1
A, B
165Homo 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
Lysine-specific demethylase 2A
C, F
47Homo sapiensMutation(s): 0 
Gene Names: KDM2A (CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KIAA1004)
EC: 1.14.11.27
Find proteins for Q9Y2K7 (Homo sapiens)
Go to Gene View: KDM2A
Go to UniProtKB:  Q9Y2K7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
D, H
86Homo sapiensMutation(s): 13 
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: 3.27 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.260 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.241α = 90.00
b = 119.582β = 98.45
c = 63.707γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaFDN 143277

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-08
    Type: Data collection, Database references
  • Version 1.2: 2018-09-19
    Type: Data collection, Database references