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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE NEDD4
A
385Homo sapiensMutation(s): 3 
Gene Names: NEDD4 (KIAA0093, NEDD4-1)
EC: 2.3.2.26
Find proteins for P46934 (Homo sapiens)
Go to Gene View: NEDD4
Go to UniProtKB:  P46934
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
POLYUBIQUITIN-B
C
76Bos taurusMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG53 (Bos taurus)
Go to Gene View: UBB
Go to UniProtKB:  P0CG53
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
POLYUBIQUITIN-B
F
76Bos taurusMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG53 (Bos taurus)
Go to Gene View: UBB
Go to UniProtKB:  P0CG53
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 196.540α = 90.00
b = 196.540β = 90.00
c = 98.770γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references
  • Version 1.2: 2013-05-15
    Type: Database references
  • Version 1.3: 2013-09-25
    Type: Database references