5C7M

CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

    Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Equipe Labellisée La Ligue Contre Le Cancer, Université de Nice-Sophia Antipolis, 151 Route St Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex, France.,Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada.,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.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G1L7, Canada.,Department of Biology, York University, Toronto, Ontario M3J1P3, Canada.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address: brenda.schulman@stjude.org.,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.,Campbell Family Cancer Research Institute, University Health Network, Toronto, ON M5G2C1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Itchy homolog
A
394Homo sapiensMutation(s): 0 
Gene Names: ITCH
EC: 2.3.2.26
Find proteins for Q96J02 (Homo sapiens)
Go to Gene View: ITCH
Go to UniProtKB:  Q96J02
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
B, C
84Homo sapiensMutation(s): 12 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.115α = 90.00
b = 121.115β = 90.00
c = 85.547γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
HKL-2000data collection
BALBESphasing
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references