NEDD4 HECT A889F structure

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structure of a Ubiquitin-Loaded Hect Ligase Reveals the Molecular Basis for Catalytic Priming

Maspero, E.Valentini, E.Mari, S.Cecatiello, V.Soffientini, P.Pasqualato, S.Polo, S.

(2013) Nat Struct Mol Biol 20: 696

  • DOI: https://doi.org/10.1038/nsmb.2566
  • Primary Citation of Related Structures:  
    4BBN, 4BE8

  • PubMed Abstract: 

    Homologous to E6-AP C terminus (HECT) E3 ligases recognize and directly catalyze ligation of ubiquitin (Ub) to their substrates. Molecular details of this process remain unknown. We report the first structure, to our knowledge, of a Ub-loaded E3, the human neural precursor cell-expressed developmentally downregulated protein 4 (Nedd4). The HECT(Nedd4)~Ub transitory intermediate provides a structural basis for the proposed sequential addition mechanism. The donor Ub, transferred from the E2, is bound to the Nedd4 C lobe with its C-terminal tail locked in an extended conformation, primed for catalysis. We provide evidence that the Nedd4-family members are Lys63-specific enzymes whose catalysis is mediated by an essential C-terminal acidic residue.

  • Organizational Affiliation

    Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE NEDD4385Homo sapiensMutation(s): 4 
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P46934 (Homo sapiens)
Explore P46934 
Go to UniProtKB:  P46934
PHAROS:  P46934
GTEx:  ENSG00000069869 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46934
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.545α = 90
b = 100.545β = 90
c = 96.45γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2013-05-15
    Changes: Database references
  • Version 1.3: 2013-08-28
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description