[English] 日本語
Yorodumi
- EMDB-48343: Structure of acid-sensing ion channel 5 without calcium, open -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48343
TitleStructure of acid-sensing ion channel 5 without calcium, open
Map dataSharpened map, nanodisc, EGTA, expanded
Sample
  • Complex: Acid-sensing ion channel 5 with calcium
    • Protein or peptide: Acid-sensing ion channel 5
KeywordsIon channel / 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: 3.47 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)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 18, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48343.png

Downloads & links

-
Map

FileDownload / File: emd_48343.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, nanodisc, EGTA, expanded
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: 0.12
Minimum - Maximum-0.001743528 - 1.6359603
Average (Standard dev.)0.0010628488 (±0.02021278)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: unsharpened map, nanodisc, EGTA, expanded

Fileemd_48343_additional_1.map
Annotationunsharpened map, nanodisc, EGTA, expanded
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half A

Fileemd_48343_half_map_1.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_48343_half_map_2.map
Annotationhalf_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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: all
Source (natural)Organism: Homo sapiens (human)

-
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: 49.257297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FDHDFAISTS FHGIHNIVQN RSKIRRVLWL VVVLGSVSLV TWQIYIRLLN YFTWPTTTSI EVQYVEKMEF PAVTFCNLNR FQTDAVAKF GVIFFLWHIV SKVLHLQEIT ANSTGSREAT DFAASHQNFS IVEFIRNKGF YLNNSTLLDC EFFGKPCSPK D FAHVFTEY ...String:
FDHDFAISTS FHGIHNIVQN RSKIRRVLWL VVVLGSVSLV TWQIYIRLLN YFTWPTTTSI EVQYVEKMEF PAVTFCNLNR FQTDAVAKF GVIFFLWHIV SKVLHLQEIT ANSTGSREAT DFAASHQNFS IVEFIRNKGF YLNNSTLLDC EFFGKPCSPK D FAHVFTEY GNCFTFNHGE TLQAKRKVSV SGRGLSLLFN VNQEAFTDNP ALGFVDAGII FVIHSPKKVP QFDGLGLLSP VG MHARVTI RQVKTVHQEY PWGECNPNIK LQNFSSYSTS GCLKECKAQH IKKQCGCVPF LLPGYGIECD LQKYFSCVSP VLD HIEFKD LCTVGTHNSS CPVSCEEIEY PATISYSSFP SQKALKYLSK KLNQSRKYIR ENLVKIEINY SDLNYKITQQ QKAV SVSEL LADLGGQLGL FCGASLITII EIIEYLFTNF

UniProtKB: Bile acid-sensitive ion channel

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 18596
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more