9Z5Q

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

Summary for 9Z5Q

• Entry DOI: 10.2210/pdb9z5q/pdb
• EMDB information: 73821
• Descriptor: Nanobody C11 (nb.C11), E3 ubiquitin-protein ligase NEDD4-like (2 entities in total)
• Functional Keywords: ubiquitin, targeted protein degradation, e3 ligase, nanobody, ligase
• Biological source: Lama glama; More
• Total number of polymer chains: 2
• Total formula weight: 70415.56

Authors

Afriyie, E.,Clarke, O.B. (deposition date: 2025-11-12, release date: 2025-12-17, Last modification date: 2026-01-28)

Primary citation

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.
Ion channel inhibition by targeted recruitment of NEDD4-2 with divalent nanobodies.
Nat Commun, 17:378-378, 2025

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 (Ca2.2; 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.

PubMed: 41353348
DOI: 10.1038/s41467-025-67068-x

Experimental method

ELECTRON MICROSCOPY (3.06 Å)