9JF7

The structure of PDPNaC1 at APO state

Summary for 9JF7

• Entry DOI: 10.2210/pdb9jf7/pdb
• EMDB information: 61429
• Descriptor: proton dissociation permeative sodium channel (PDPNaC1) (1 entity in total)
• Functional Keywords: pdpnac1, membrane protein, trimer
• Biological source: Scolopendra mutilans
• Total number of polymer chains: 3
• Total formula weight: 149433.08

Authors

Yuan, L.,Shang, J.,Dong, W. (deposition date: 2024-09-04, release date: 2025-08-20, Last modification date: 2025-12-31)

Primary citation

Dong, W.,Yuan, L.,Shang, J.,Yang, F.,Yang, S.,Lu, X.,Wang, Q.,Luo, A.,Geng, J.,Cheng, J.,Li, R.,Wang, Y.
A proton-gated channel identified in the centipede antenna.
Embo Rep., 26:6083-6095, 2025

PubMed Abstract: Acid sensing is essential for various biological processes in animals, yet it exhibits species-specific characteristics. In this study, we identified a proton-dissociation-permeated sodium channel (PDPNaC1) in the antennal sensory neurons of the centipede Scolopendra subspinipes mutilans. PDPNaC1, which is permeable to monovalent cations, assembles as a homotrimer. Unlike most proton-gated channels, where proton binding induces currents, PDPNaC1's transient ion-permeable state is triggered by proton dissociation. By resolving the high-resolution cryo-electron microscopy (cryo-EM) structure of PDPNaC1, combined with mutagenesis and electrophysiological analyses, we identified Gly378, rather than the Gly-Ala-Ser tract, as a key determinant of ion selectivity. Furthermore, Ser376, located in the ion-permeable pathway, likely serves as a proton-binding site, leading to an H-blocking effect that results in proton-dissociated currents. Thus, the identification of PDPNaC1 suggests the remarkable diversity of proton responses and molecular mechanisms in DEG/ENaC family.

PubMed: 41116071
DOI: 10.1038/s44319-025-00606-2

Experimental method

ELECTRON MICROSCOPY (3.03 Å)