5O6T

BIRC4 RING in complex with dimeric ubiquitin variant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.0 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 XIAP
A, B
66Homo sapiensMutation(s): 0 
Gene Names: XIAP (API3, BIRC4, IAP3)
EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens)
Go to Gene View: XIAP
Go to UniProtKB:  P98170
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C, D
80N/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, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.715α = 90.00
b = 69.972β = 90.00
c = 109.747γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
xia2data reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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