5O76

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.molcel.2017.09.027
  • Primary Citation of Related Structures:  
    5O6S, 5O6T, 5O75, 5O76

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CBL
A, C
391Homo sapiensMutation(s): 1 
Gene Names: CBLCBL2RNF55
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P22681 (Homo sapiens)
Explore P22681 
Go to UniProtKB:  P22681
PHAROS:  P22681
GTEx:  ENSG00000110395 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22681
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine protein kinase ZAP70 peptide
B, D
12Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43403 (Homo sapiens)
Explore P43403 
Go to UniProtKB:  P43403
PHAROS:  P43403
GTEx:  ENSG00000115085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43403
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UbV.pCBL ubiquitin variant
E, F
82Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.79α = 90
b = 101.281β = 90
c = 117.339γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description