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- EMDB-48342: Structure of acid-sensing ion channel 5 with calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-48342
TitleStructure of acid-sensing ion channel 5 with calcium
Map dataUnsharpened Map
Sample
  • Complex: acid-sensing ion channel 5 with calcium
    • Protein or peptide: Acid-sensing ion channel 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIon channel / MEMBRANE PROTEIN / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFreitas MM / Gouaux E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31 NS120713 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 18, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48342.png

Downloads & links

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Map

FileDownload / File: emd_48342.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0799
Minimum - Maximum-0.19717765 - 0.5107675
Average (Standard dev.)0.0003849263 (±0.012928133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 283.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48342_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map, B

Fileemd_48342_half_map_1.map
AnnotationHalf map, B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map, A

Fileemd_48342_half_map_2.map
AnnotationHalf map, A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : acid-sensing ion channel 5 with calcium

EntireName: acid-sensing ion channel 5 with calcium
Components
  • Complex: acid-sensing ion channel 5 with calcium
    • Protein or peptide: Acid-sensing ion channel 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: acid-sensing ion channel 5 with calcium

SupramoleculeName: acid-sensing ion channel 5 with calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Acid-sensing ion channel 5

MacromoleculeName: Acid-sensing ion channel 5 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.531012 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQTEKSKVY AENGLLEKIK LCLSKKPLPS PTERKKFDHD FAISTSFHGI HNIVQNRSKI RRVLWLVVVL GSVSLVTWQI YIRLLNYFT WPTTTSIEVQ YVEKMEFPAV TFCNLNRFQT DAVAKFGVIF FLWHIVSKVL HLQEITANST GSREATDFAA S HQNFSIVE ...String:
MEQTEKSKVY AENGLLEKIK LCLSKKPLPS PTERKKFDHD FAISTSFHGI HNIVQNRSKI RRVLWLVVVL GSVSLVTWQI YIRLLNYFT WPTTTSIEVQ YVEKMEFPAV TFCNLNRFQT DAVAKFGVIF FLWHIVSKVL HLQEITANST GSREATDFAA S HQNFSIVE FIRNKGFYLN NSTLLDCEFF GKPCSPKDFA HVFTEYGNCF TFNHGETLQA KRKVSVSGRG LSLLFNVNQE AF TDNPALG FVDAGIIFVI HSPKKVPQFD GLGLLSPVGM HARVTIRQVK TVHQEYPWGE CNPNIKLQNF SSYSTSGCLK ECK AQHIKK QCGCVPFLLP GYGIECDLQK YFSCVSPVLD HIEFKDLCTV GTHNSSCPVS CEEIEYPATI SYSSFPSQKA LKYL SKKLN QSRKYIRENL VKIEINYSDL NYKITQQQKA VSVSELLADL GGQLGLFCGA SLITIIEIIE YLFTNFYWIC IFFLL KISE MTQWTPPPQN HLGNKNRIEE C

UniProtKB: Bile acid-sensitive ion channel

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration3.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold-Q9NY37-F1-V4
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 52213
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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