5HPS

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1 and UbV P1.1

• PDB DOI:  https://doi.org/10.2210/pdb5HPS/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-20 Released: 2016-03-16 
• Deposition Author(s): Wu, K.-P., Mercredi, P.Y., Schulman, B.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

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

• PubMed: 26949039 
• DOI: https://doi.org/10.1016/j.molcel.2016.02.005
• Primary Citation of Related Structures:  
  5C7J, 5C7M, 5HPK, 5HPL, 5HPS, 5HPT


• 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 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.

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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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.65 kDa 
• Atom Count: 3,817 
• Modelled Residue Count: 447 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WWP1 HECT	A	383	Homo sapiens	Mutation(s): 0  Gene Names: WWP1 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0M0 (Homo sapiens) Explore Q9H0M0  Go to UniProtKB:  Q9H0M0
PHAROS:  Q9H0M0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin variant P1.1	B	83	Homo sapiens	Mutation(s): 0  Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.914	α = 90
b = 44.908	β = 96.07
c = 60.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Wu, K.-P., Mercredi, P.Y., Schulman, B.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103403

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2016-04-13
  Changes: Source and taxonomy
• Version 1.3: 2016-04-20
  Changes: Database references
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence