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- PDB-9mlv: Structure of acid-sensing ion channel 5 without calcium, closed -

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Basic information

Entry
Database: PDB / ID: 9mlv
TitleStructure of acid-sensing ion channel 5 without calcium, closed
ComponentsAcid-sensing ion channel 5
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homology
Function and homology information


bile acid-gated sodium channel activity / sodium ion import across plasma membrane / proton channel activity / ligand-gated sodium channel activity / neuronal action potential / sodium ion transmembrane transport / Stimuli-sensing channels / apical plasma membrane / plasma membrane
Similarity search - Function
Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Bile acid-sensitive ion channel
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFreitas, M.M. / Gouaux, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS120713 United States
National Science Foundation (NSF, United States)1000271223 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2025
Title: The bile acid-sensitive ion channel is gated by Ca-dependent conformational changes in the transmembrane domain.
Authors: Makayla M Freitas / Eric Gouaux /
Abstract: The bile acid-sensitive ion channel (BASIC) is the least understood member of the mammalian epithelial Na channel/degenerin (ENaC/DEG) superfamily of ion channels, which are involved in a variety of ...The bile acid-sensitive ion channel (BASIC) is the least understood member of the mammalian epithelial Na channel/degenerin (ENaC/DEG) superfamily of ion channels, which are involved in a variety of physiological processes. While some members of this superfamily, including BASIC, are inhibited by extracellular Ca (Ca), the molecular mechanism underlying Ca modulation remains unclear. Here, by determining the structure of human BASIC (hBASIC) in the presence and absence of Ca using single-particle cryo-electron microscopy (cryo-EM), we reveal Ca-dependent conformational changes in the transmembrane domain and β-linkers. Electrophysiological experiments further show that a glutamate residue in the extracellular vestibule of the pore underpins the Ca-binding site, whose occupancy determines the conformation of the pore and therefore ion flow through the channel. These results reveal the molecular principles governing gating of BASIC and its regulation by Ca ions, demonstrating that Ca ions modulate BASIC function via changes in protein conformation rather than solely from a pore-block, as proposed for other members of this superfamily.
History
DepositionDec 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid-sensing ion channel 5
C: Acid-sensing ion channel 5
B: Acid-sensing ion channel 5


Theoretical massNumber of molelcules
Total (without water)172,5933
Polymers172,5933
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 Acid-sensing ion channel 5 / ASIC5 / Amiloride-sensitive cation channel 5 / Human intestine Na(+) channel / HINaC


Mass: 57531.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASIC5, ACCN5, HINAC / Production host: Homo sapiens (human) / References: UniProt: Q9NY37
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: Acid-sensing ion channel 5 without calcium / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 3.5 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC3CTF correction
7Coot0.9.8.92model fitting
9PHENIX1.2.1model refinement
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15003 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 191.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039939
ELECTRON MICROSCOPYf_angle_d0.469613515
ELECTRON MICROSCOPYf_chiral_restr0.03971530
ELECTRON MICROSCOPYf_plane_restr0.00331737
ELECTRON MICROSCOPYf_dihedral_angle_d4.78461338

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