Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 62.83 kDa 
• Atom Count: 4492 
• Modelled Residue Count: 530 
• Deposited Residue Count: 537 
• Unique protein chains: 3

4BBN

NEDD4 HECT-Ub:Ub complex

• DOI: 10.2210/pdb4BBN/pdb

• Classification: LIGASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-09-27 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: 2.51 Å
• R-Value Free: 0.224 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

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: 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.

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Organizational Affiliation: 

Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE NEDD4	A	385	Homo sapiens	Mutation(s): 3  Gene Names: NEDD4, KIAA0093, NEDD4-1, PIG53 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 GTEx:  ENSG00000069869

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYUBIQUITIN-B	B [auth C]	76	Bos taurus	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG53 (Bos taurus) Explore P0CG53  Go to UniProtKB:  P0CG53

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYUBIQUITIN-B	C [auth F]	76	Bos taurus	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG53 (Bos taurus) Explore P0CG53  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 
• R-Value Observed: 0.179 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.54	α = 90
b = 196.54	β = 90
c = 98.77	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-27 
• 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: 2013-09-25
  Changes: Database references