5HPT

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.

Zhang, W.Wu, K.P.Sartori, M.A.Kamadurai, H.B.Ordureau, A.Jiang, C.Mercredi, P.Y.Murchie, R.Hu, J.Persaud, A.Mukherjee, M.Li, N.Doye, A.Walker, J.R.Sheng, Y.Hao, Z.Li, Y.Brown, K.R.Lemichez, E.Chen, J.Tong, Y.Harper, J.W.Moffat, J.Rotin, D.Schulman, B.A.Sidhu, S.S.

(2016) Mol.Cell 62: 121-136

  • DOI: 10.1016/j.molcel.2016.02.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HECT-family E3 ligases ubiquitinate protein substrates to control virtually every eukaryotic process and are misregulated in numerous diseases. Nonetheless, understanding of HECT E3s is limited by a paucity of selective and potent modulators. To over ...

    HECT-family E3 ligases ubiquitinate protein substrates to control virtually every eukaryotic process and are misregulated in numerous diseases. Nonetheless, understanding of HECT E3s is limited by a paucity of selective and potent modulators. To overcome this challenge, we systematically developed ubiquitin variants (UbVs) that inhibit or activate HECT E3s. Structural analysis of 6 HECT-UbV complexes revealed UbV inhibitors hijacking the E2-binding site and activators occupying a ubiquitin-binding exosite. Furthermore, UbVs unearthed distinct regulation mechanisms among NEDD4 subfamily HECTs and proved useful for modulating therapeutically relevant targets of HECT E3s in cells and intestinal organoids, and in a genetic screen that identified a role for NEDD4L in regulating cell migration. Our work demonstrates versatility of UbVs for modulating activity across an E3 family, defines mechanisms and provides a toolkit for probing functions of HECT E3s, and establishes a general strategy for systematic development of modulators targeting families of signaling proteins.


    Organizational Affiliation

    Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEDD4-like E3 ubiquitin-protein ligase WWP1
A, D, G
383Homo sapiensMutation(s): 0 
Gene Names: WWP1
EC: 2.3.2.26
Find proteins for Q9H0M0 (Homo sapiens)
Go to Gene View: WWP1
Go to UniProtKB:  Q9H0M0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin variant P2.3
B, E, H
83Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
C, F
161Homo sapiensMutation(s): 0 
Gene Names: UBE2L3 (UBCE7, UBCH7)
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Go to Gene View: UBE2L3
Go to UniProtKB:  P68036
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B, E, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 114.005α = 90.00
b = 118.897β = 90.00
c = 158.663γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-04-20
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations