9JF7 | pdb_00009jf7

The structure of PDPNaC1 at APO state

• PDB DOI: https://doi.org/10.2210/pdb9JF7/pdb
• EM Map EMD-61429: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Scolopendra mutilans
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-04 Released: 2025-08-20 
• Deposition Author(s): Yuan, L., Shang, J., Dong, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A proton-gated channel identified in the centipede antenna.

Dong, W., Yuan, L., Shang, J., Yang, F., Yang, S., Lu, X., Wang, Q., Luo, A., Geng, J., Cheng, J., Li, R., Wang, Y.

(2025) EMBO Rep 

• PubMed: 41116071 
• DOI: https://doi.org/10.1038/s44319-025-00606-2
• Primary Citation of Related Structures:  
  9JF7


• 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.

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Organizational Affiliation: 
• College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang, China.
Key Laboratory of National Forestry and Grassland Administration on Wildlife Protection, Harbin, Heilongjiang, China.
Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin, Heilongjiang, China.
Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang, China. [e-mail].
Key Laboratory of National Forestry and Grassland Administration on Wildlife Protection, Harbin, Heilongjiang, China. [e-mail].
Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin, Heilongjiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 149.43 kDa 
• Atom Count: 8,592 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
proton dissociation permeative sodium channel (PDPNaC1)	A, B, C	421	Scolopendra mutilans	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Yuan, L., Shang, J., Dong, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32370437

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Data collection, Database references