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GeezerVison is showing www.rcsb.org — RCSB PDB - 4Y07: Crystal structure of the HECT domain of human WWP2

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 4Y07 | pdb_00004y07

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.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.285 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Y07

This is version 1.1 of the entry. See complete history. 

Literature

  • Download Mendeley

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 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1107/S2053230X1501554X
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Institutes of Biomedical Sciences and School of Basic Medical Sciences, Fudan University, People's Republic of China.
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

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

Find Similar Assemblies

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NEDD4-like E3 ubiquitin-protein ligase WWP2
A
374Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00308
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.285 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.765α = 90
b = 61.765β = 90
c = 242.943γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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