4BBN

NEDD4 HECT-Ub:Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE NEDD4A385Homo sapiensMutation(s): 3 
Gene Names: NEDD4KIAA0093NEDD4-1PIG53
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
Find proteins for P46934 (Homo sapiens)
Explore P46934 
Go to UniProtKB:  P46934
NIH Common Fund Data Resources
PHAROS  P46934
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-BC76Bos taurusMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG53 (Bos taurus)
Explore P0CG53 
Go to UniProtKB:  P0CG53
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-BF76Bos taurusMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG53 (Bos taurus)
Explore P0CG53 
Go to UniProtKB:  P0CG53
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.54α = 90
b = 196.54β = 90
c = 98.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: 2013-09-25
    Changes: Database references