5O76

Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.473 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.

Gabrielsen, M.Buetow, L.Nakasone, M.A.Ahmed, S.F.Sibbet, G.J.Smith, B.O.Zhang, W.Sidhu, S.S.Huang, D.T.

(2017) Mol. Cell 68: 456-470.e10

  • DOI: 10.1016/j.molcel.2017.09.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RING and U-box E3 ubiquitin ligases regulate diverse eukaryotic processes and have been implicated in numerous diseases, but targeting these enzymes remains a major challenge. We report the development of three ubiquitin variants (UbVs), each binding ...

    RING and U-box E3 ubiquitin ligases regulate diverse eukaryotic processes and have been implicated in numerous diseases, but targeting these enzymes remains a major challenge. We report the development of three ubiquitin variants (UbVs), each binding selectively to the RING or U-box domain of a distinct E3 ligase: monomeric UBE4B, phosphorylated active CBL, or dimeric XIAP. Structural and biochemical analyses revealed that UbVs specifically inhibited the activity of UBE4B or phosphorylated CBL by blocking the E2∼Ub binding site. Surprisingly, the UbV selective for dimeric XIAP formed a dimer to stimulate E3 activity by stabilizing the closed E2∼Ub conformation. We further verified the inhibitory and stimulatory functions of UbVs in cells. Our work provides a general strategy to inhibit or activate RING/U-box E3 ligases and provides a resource for the research community to modulate these enzymes.


    Organizational Affiliation

    Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada. Electronic address: wx.zhang@mail.utoronto.ca.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada. Electronic address: sachdev.sidhu@utoronto.ca.,Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK. Electronic address: d.huang@beatson.gla.ac.uk.,Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase CBL
A, C
391Homo sapiensMutation(s): 1 
Gene Names: CBL (CBL2, RNF55)
EC: 2.3.2.27
Find proteins for P22681 (Homo sapiens)
Go to Gene View: CBL
Go to UniProtKB:  P22681
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosine protein kinase ZAP70 peptide
B, D
12Homo sapiensMutation(s): 0 
Gene Names: ZAP70 (SRK)
EC: 2.7.10.2
Find proteins for P43403 (Homo sapiens)
Go to Gene View: ZAP70
Go to UniProtKB:  P43403
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UbV.pCBL ubiquitin variant
E, F
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.473 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.790α = 90.00
b = 101.281β = 90.00
c = 117.339γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
BUSTERrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC596/A23278
European Research CouncilUnited Kingdom647849

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Source and taxonomy