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- EMDB-47510: Human ASIC1a at pH 5.7 with rotated, domain-swapped transmembrane... -

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Basic information

Entry
Database: EMDB / ID: EMD-47510
TitleHuman ASIC1a at pH 5.7 with rotated, domain-swapped transmembrane domain
Map dataMap of human ASIC1a at pH 5.7 with rotated, domain-swapped transmembrane domain
Sample
  • Complex: Homotrimeric complex of acid-sensing channel 1a
    • Protein or peptide: Acid-sensing ion channel 1
KeywordsIon channel / Trimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / cellular response to pH / ligand-gated sodium channel activity / sodium ion transport / regulation of postsynapse assembly / sodium ion transmembrane transport / postsynaptic density membrane / Stimuli-sensing channels ...monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / cellular response to pH / ligand-gated sodium channel activity / sodium ion transport / regulation of postsynapse assembly / sodium ion transmembrane transport / postsynaptic density membrane / Stimuli-sensing channels / calcium ion transport / dendrite / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsHartfield KA / Cahill J / Baconguis I
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138862 United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Conformational plasticity of human acid-sensing ion channel 1a.
Authors: James Cahill / Kimberly A Hartfield / Stephanie Andrea Heusser / Nadine Ritter / Mette Homann Poulsen / Craig Yoshioka / Stephan Alexander Pless / Isabelle Baconguis /
Abstract: Acid-sensing ion channels (ASICs) are typically activated by acidic environments and contribute to nociception and synaptic plasticity. ASIC1a is the most abundant subunit in the central nervous ...Acid-sensing ion channels (ASICs) are typically activated by acidic environments and contribute to nociception and synaptic plasticity. ASIC1a is the most abundant subunit in the central nervous system and forms homomeric channels permeable to Na and Ca, making it a compelling therapeutic target for acidotic pathologies including stroke and traumatic brain injury. However, a complete conformational library of human ASIC1a has yet to be described. Here we show that human ASIC1a adopts six major conformations, resolved by cryo-electron microscopy across a pH range between 8.5 and 5.7 and in the presence of a toxin agonist and a gating-modifying amino acid substitution. These major conformations establish linear transmembrane helices to be associated with an open state, delineate mechanistic differences between proton and toxin activation and demonstrate that desensitization involves unexpected conformational diversity in the transmembrane domain. Together, they provide a three-dimensional framework to integrate previous structure-function studies on ASIC.
History
DepositionOct 24, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47510.png

Downloads & links

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Map

FileDownload / File: emd_47510.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of human ASIC1a at pH 5.7 with rotated, domain-swapped transmembrane domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.176 Å		0.84 Å/pix.
x 384 pix.
= 322.176 Å		0.84 Å/pix.
x 384 pix.
= 322.176 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29563427 - 0.71102273
Average (Standard dev.)0.00045914485 (±0.014318123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47510_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B corresponding to the primary map

Fileemd_47510_half_map_1.map
AnnotationHalf map B corresponding to the primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A corresponding to the primary map

Fileemd_47510_half_map_2.map
AnnotationHalf map A corresponding to the primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotrimeric complex of acid-sensing channel 1a

EntireName: Homotrimeric complex of acid-sensing channel 1a
Components
  • Complex: Homotrimeric complex of acid-sensing channel 1a
    • Protein or peptide: Acid-sensing ion channel 1

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Supramolecule #1: Homotrimeric complex of acid-sensing channel 1a

SupramoleculeName: Homotrimeric complex of acid-sensing channel 1a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Acid-sensing ion channel 1

MacromoleculeName: Acid-sensing ion channel 1 / type: protein_or_peptide / ID: 1
Details: Thrombin cleavage product of construct with N-terminal fusion of 8xHis-EGFP-Thrombin site
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.252625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGRMELKAEE EEVGGVQPVS IQAFASSSTL HGLAHIFSYE RLSLKRALWA LCFLGSLAVL LCVCTERVQY YFHYHHVTKL DEVAASQLT FPAVTLCNLN EFRFSQVSKN DLYHAGELLA LLNNRYEIPD TQMADEKQLE ILQDKANFRS FKPKPFNMRE F YDRAGHDI ...String:
GGRMELKAEE EEVGGVQPVS IQAFASSSTL HGLAHIFSYE RLSLKRALWA LCFLGSLAVL LCVCTERVQY YFHYHHVTKL DEVAASQLT FPAVTLCNLN EFRFSQVSKN DLYHAGELLA LLNNRYEIPD TQMADEKQLE ILQDKANFRS FKPKPFNMRE F YDRAGHDI RDMLLSCHFR GEVCSAEDFK VVFTRYGKCY TFNSGRDGRP RLKTMKGGTG NGLEIMLDIQ QDEYLPVWGE TD ETSFEAG IKVQIHSQDE PPFIDQLGFG VAPGFQTFVA CQEQRLIYLP PPWGTCKAVT MDSDLDFFDS YSITACRIDC ETR YLVENC NCRMVHMPGD APYCTPEQYK ECADPALDFL VEKDQEYCVC EMPCNLTRYG KELSMVKIPS KASAKYLAKK FNKS EQYIG ENILVLDIFF EVLNYETIEQ KKAYEIAGLL GDIGGQMGLF IGASILTVLE LFDYAYEVIK HKLCRRGKCQ KEAKR SSAD KGVALSLDDV KRHNPCESLR GHPAGMTYAA NILPHHPARG TFEDFTC

UniProtKB: Acid-sensing ion channel 1

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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

Concentration4 mg/mL
BufferpH: 5.7
Component:
ConcentrationFormulaName
50.0 mMNa2HPO4/NaH2PO4sodium phosphate
200.0 mMNaClsodium chloride
1.0 mg/mLdigitonin
1.0 mMC9H15O6PTris(2-carboxyethyl)phosphine hydrochloride
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse sample of homotrimeric ASIC1a

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 84730
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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