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- PDB-9jf7: The structure of PDPNaC1 at APO state -

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Entry
Database: PDB / ID: 9jf7
TitleThe structure of PDPNaC1 at APO state
Componentsproton dissociation permeative sodium channel (PDPNaC1)
KeywordsMEMBRANE PROTEIN / PDPNaC1 / Trimer
Biological speciesScolopendra mutilans (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsYuan, L. / Shang, J. / Dong, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370437 China
CitationJournal: EMBO Rep / Year: 2025
Title: A proton-gated channel identified in the centipede antenna.
Authors: Wenqi Dong / Licheng Yuan / Jiangming Shang / Fan Yang / Shilong Yang / Xiancui Lu / Qian Wang / Anna Luo / Jiheng Geng / Jiatong Cheng / Runze Li / Yunfei Wang /
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 ...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.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: proton dissociation permeative sodium channel (PDPNaC1)
B: proton dissociation permeative sodium channel (PDPNaC1)
C: proton dissociation permeative sodium channel (PDPNaC1)


Theoretical massNumber of molelcules
Total (without water)149,4333
Polymers149,4333
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein proton dissociation permeative sodium channel (PDPNaC1)


Mass: 49811.027 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scolopendra mutilans (arthropod) / Cell (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The structure of PDPNaC1 at APO state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Scolopendra mutilans (arthropod)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 6 sec. / Electron dose: 52 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121831 / Symmetry type: POINT

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