9GIM | pdb_00009gim

Full-lenght Nedd4-2 E3 ubiquitin ligase in presence of Ca2+

• PDB DOI: https://doi.org/10.2210/pdb9GIM/pdb
• EM Map EMD-51374: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-19 Released: 2025-06-04 
• Deposition Author(s): Kosek, D., Janosev, M., Obsil, T., Obsilova, V.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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

• PubMed: 40419858 
• DOI: https://doi.org/10.1038/s41467-025-60207-4
• Primary Citation 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.

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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.
Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czech Republic.
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. [e-mail].
Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czech Republic. [e-mail].
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. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 110.47 kDa 
• Atom Count: 5,321 
• Modeled Residue Count: 639 
• Deposited Residue Count: 959 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 5 of E3 ubiquitin-protein ligase NEDD4-like	A	959	Homo sapiens	Mutation(s): 0  Gene Names: NEDD4L, KIAA0439, NEDL3 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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.1.
MODEL REFINEMENT	PHENIX	1.19.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Kosek, D., Janosev, M., Obsil, T., Obsilova, V.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	23-046865

Revision History  

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