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.




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