9GIK | pdb_00009gik

Full-lenght Nedd4-2 E3 ubiquitin ligase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins.

Janosev, M.Kosek, D.Tekel, A.Joshi, R.Honzejkova, K.Pohl, P.Obsil, T.Obsilova, V.

(2025) Nat Commun 16: 4875-4875

  • DOI: https://doi.org/10.1038/s41467-025-60207-4
  • Primary Citation of Related Structures:  
    9GIK, 9GIM

  • PubMed Abstract: 

    Nedd4-2 E3 ligase regulates Na + homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney diseases. However, Nedd4-2 regulation remains mostly unclear. The present study aims at elucidating Nedd4-2 regulation by structurally characterizing Nedd4-2 and its complexes using several biophysical techniques. Our cryo-EM reconstruction shows that the C2 domain blocks the E2-binding surface of the HECT domain. This blockage, ubiquitin-binding exosite masking by the WW1 domain, catalytic C922 blockage and HECT domain stabilization provide the structural basis for Nedd4-2 autoinhibition. Furthermore, Ca 2+ -dependent C2 membrane binding disrupts C2/HECT interactions, but not Ca 2+ alone, whereas 14-3-3 protein binds to a flexible region of Nedd4-2 containing the WW2 and WW3 domains, thereby inhibiting its catalytic activity and membrane binding. Overall, our data provide key mechanistic insights into Nedd4-2 regulation toward fostering the development of strategies targeting Nedd4-2 function.


  • Organizational Affiliation
    • Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 5 of E3 ubiquitin-protein ligase NEDD4-like959Homo sapiensMutation(s): 0 
Gene Names: NEDD4LKIAA0439NEDL3
EC: 2.3.2.26 (PDB Primary Data), 2.3.2.36 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU5 (Homo sapiens)
Explore Q96PU5 
Go to UniProtKB:  Q96PU5
PHAROS:  Q96PU5
GTEx:  ENSG00000049759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PU5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1.
MODEL REFINEMENTPHENIX1.19.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic23-046865

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release