9Z5Q | pdb_00009z5q

HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11

  • Classification: LIGASE
  • Organism(s): Lama glama, Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2025-11-12 Released: 2025-12-17 
  • Deposition Author(s): Afriyie, E., Clarke, O.B.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Heart Association, National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, other
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z5Q

This is version 1.1 of the entry. See complete history

Literature

Ion channel inhibition by targeted recruitment of NEDD4-2 with divalent nanobodies.

Darko-Boateng, A.Afriyie, E.Morgenstern, T.J.Shanmugam, S.K.Zou, X.Laloudakis, Y.D.Choudhury, P.Desai, M.Kass, R.S.Vallese, F.Clarke, O.B.Colecraft, H.M.

(2025) Nat Commun 17: 378-378

  • DOI: https://doi.org/10.1038/s41467-025-67068-x
  • Primary Citation Related Structures: 
    9Z5Q

  • PubMed Abstract: 

    Targeted protein degradation/downregulation (TPD/TPDR) is a disruptive paradigm for developing therapeutics. <2% of ~600 E3 ligases have been exploited for this modality, and efficacy for multi-subunit ion channels has not been demonstrated. NEDD4-2 E3 ligase regulates myriad ion channels, but its utility for TPD/TPDR is uncertain due to complex regulatory mechanisms. Here, we identify a nanobody that binds NEDD4-2 HECT domain without disrupting catalysis sites as revealed by cryo-electron microscopy and in vitro ubiquitination assays. Recruiting NEDD4-2 to diverse ion channels (Ca V 2.2; KCNQ1; and epithelial Na + channel, ENaC, with a Liddle syndrome mutation) using divalent nanobodies (DiVas) strongly suppresses their surface density and function. Global proteomics indicates DiVa recruitment of endogenous NEDD4-2 to KCNQ1-YFP yields dramatically lower off-target effects compared to NEDD4-2 overexpression. The results establish utility of NEDD4-2 recruitment for TPD/TPDR, validate ion channels as susceptible to this modality, and introduce a general method to generate ion channel inhibitors.


  • Organizational Affiliation
    • Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 70.42 kDa 
  • Atom Count: 4,430 
  • Modeled Residue Count: 539 
  • Deposited Residue Count: 608 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody C11 (nb.C11)162Lama glamaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase NEDD4-like446Homo 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXv1.21-5207
RECONSTRUCTIONcryoSPARCv4.4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesRO1-HL121253
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesRO1-HL142111
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-NS126850
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01-HL164319
American Heart AssociationUnited States20PRE35210815
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesF31 DK118866
American Heart AssociationUnited StatesPOST1019343

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references