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- EMDB-61429: The structure of PDPNaC1 at APO state -

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Basic information

Entry
Database: EMDB / ID: EMD-61429
TitleThe structure of PDPNaC1 at APO state
Map data
Sample
  • Complex: The structure of PDPNaC1 at APO state
    • Protein or peptide: proton dissociation permeative sodium channel (PDPNaC1)
KeywordsPDPNaC1 / Membrane protein / Trimer
Biological speciesScolopendra mutilans (arthropod)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsYuan L / Shang J / Dong W
Funding support China, 1 items
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, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61429.png

Downloads & links

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Map

FileDownload / File: emd_61429.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.8822574 - 1.0285901
Average (Standard dev.)-0.00011544901 (±0.032333415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61429_half_map_1.map
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Half map: #1

Fileemd_61429_half_map_2.map
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Sample components

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Entire : The structure of PDPNaC1 at APO state

EntireName: The structure of PDPNaC1 at APO state
Components
  • Complex: The structure of PDPNaC1 at APO state
    • Protein or peptide: proton dissociation permeative sodium channel (PDPNaC1)

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Supramolecule #1: The structure of PDPNaC1 at APO state

SupramoleculeName: The structure of PDPNaC1 at APO state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Scolopendra mutilans (arthropod)

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

MacromoleculeName: proton dissociation permeative sodium channel (PDPNaC1)
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Scolopendra mutilans (arthropod)
Molecular weightTheoretical: 49.811027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSNSNVETFF KSSSEKNKNN FKEISCCFKI SNEERSLPFQ LIWSGIIIIS CIGMFWNVVE NIKLYFYSSP SVKFEYIKND SLYFPAITI CPFLLNWNPF FTESISFFPE MNDIFEIIET NEYDMLYLWN KTDEYFQYDD SYVYQDALIE EDEFDRSSII P NTEIMSVS ...String:
MSNSNVETFF KSSSEKNKNN FKEISCCFKI SNEERSLPFQ LIWSGIIIIS CIGMFWNVVE NIKLYFYSSP SVKFEYIKND SLYFPAITI CPFLLNWNPF FTESISFFPE MNDIFEIIET NEYDMLYLWN KTDEYFQYDD SYVYQDALIE EDEFDRSSII P NTEIMSVS GKCHMYSLEE PVYIGNAIPN ILIVYNHSKI YKDKWIKVLI HSIEDKLTSH FFAINVGVDS LLQQMTEVNF QV IQKINLN LSNNPCLFPE EVDKCFKKCL DNFMFKDLSR IHKCRLPFMD YPPDIPYCNY TNFPQMYTRF NKILKGFNKT NCL CPRKCR ETRYEIQYQF NIGGFNNQTF IKITSRNSIT LETEYWSYNF YSLLSDIGGS LGLFLGASIL SMCEIMQKIL RNFC MYSLS LKNRVLSRNS VHKINY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121831
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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