4Y07

Crystal structure of the HECT domain of human WWP2

• PDB DOI: https://doi.org/10.2210/pdb4Y07/pdb

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


• Deposited: 2015-02-05 Released: 2015-11-04 
• Deposition Author(s): Gong, W., Li, J., Li, Z., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.285 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

Structure of the HECT domain of human WWP2

Gong, W., Zhang, X., Zhang, W., Li, J., Li, Z.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1251-1257

• PubMed: 26457515 
• DOI: https://doi.org/10.1107/S2053230X1501554X
• Primary Citation of Related Structures:  
  4Y07


• PubMed Abstract: 
  

  WWP2 is a HECT-domain ubiquitin ligase of the Nedd4 family, which is involved in various important biological processes, such as protein degradation, membrane-protein sorting and transportation, the immune response, pluripotency of embryonic stem cells, tumourigenesis and metastasis. The HECT domain provides the intrinsic ubiquitin ligase activity of WWP2. Here, the expression, purification, crystallization and crystallographic analysis of the HECT domain of human WWP2 (HECT(WWP2)) are reported. HECT(WWP2) has been crystallized and the crystals diffracted to 2.50 Å resolution. They belonged to space group P41212 and the structure has been solved via molecular replacement. The overall structure of HECT(WWP2) has an inverted T-shape. This structure displays a high degree of conservation with previously published structures of Nedd4 subfamily members.

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Organizational Affiliation: 

Institutes of Biomedical Sciences and School of Basic Medical Sciences, Fudan University, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.77 kDa 
• Atom Count: 2,908 
• Modelled Residue Count: 333 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD4-like E3 ubiquitin-protein ligase WWP2	A	374	Homo sapiens	Mutation(s): 0  Gene Names: WWP2 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00308 (Homo sapiens) Explore O00308  Go to UniProtKB:  O00308
PHAROS:  O00308 GTEx:  ENSG00000198373

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.285 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.765	α = 90
b = 61.765	β = 90
c = 242.943	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Gong, W., Li, J., Li, Z., Xu, Y.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description