4BE8 | pdb_00004be8

NEDD4 HECT A889F structure

• PDB DOI: https://doi.org/10.2210/pdb4BE8/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-03-06 Released: 2013-05-01 
• Deposition Author(s): Maspero, E., Valentini, E., Mari, S., Cecatiello, V., Polo, S., Pasqualato, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

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

• PubMed: 23644597 
• DOI: https://doi.org/10.1038/nsmb.2566
• Primary Citation 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.

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Organizational Affiliation: 
• Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.71 kDa 
• Atom Count: 3,124 
• Modeled Residue Count: 378 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE NEDD4	A	385	Homo sapiens	Mutation(s): 4  EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P46934 (Homo sapiens) Explore P46934  Go to UniProtKB:  P46934
PHAROS:  P46934 GTEx:  ENSG00000069869

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.545	α = 90
b = 100.545	β = 90
c = 96.45	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Maspero, E., Valentini, E., Mari, S., Cecatiello, V., Polo, S., Pasqualato, S.

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: 2013-08-28
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description