5C7J

CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5C7J, 5C7M, 5HPT, 5HPS, 5HPL, 5HPK

  • 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; Department of Molecular Genetics, University of Toronto, 1 King's College Cir, Toronto, ON M5S1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase NEDD4AB382Homo sapiensMutation(s): 0 
Gene Names: NEDD4KIAA0093NEDD4-1PIG53
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
Find proteins for P46934 (Homo sapiens)
Explore P46934 
Go to UniProtKB:  P46934
NIH Common Fund Data Resources
PHAROS  P46934
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CCD92Homo sapiensMutation(s): 8 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.867α = 90
b = 139.867β = 90
c = 59.386γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Database references, Derived calculations, Structure summary