[English] 日本語
Yorodumi
- EMDB-47504: Human ASIC1a at pH 7.5 with domain-swapped transmembrane domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47504
TitleHuman ASIC1a at pH 7.5 with domain-swapped transmembrane domain
Map dataMap of human ASIC1a at pH 7.5, Conformation 1
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 / negative regulation of neurotransmitter secretion / response to acidic pH / neurotransmitter secretion / ligand-gated sodium channel activity / sodium ion transport / associative learning ...monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / cellular response to pH / negative regulation of neurotransmitter secretion / response to acidic pH / neurotransmitter secretion / ligand-gated sodium channel activity / sodium ion transport / associative learning / regulation of postsynapse assembly / behavioral fear response / sodium ion transmembrane transport / response to amphetamine / regulation of membrane potential / postsynaptic density membrane / calcium ion transmembrane transport / Stimuli-sensing channels / memory / presynapse / dendrite / glutamatergic synapse / cell surface / Golgi apparatus / 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: 3.09 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: To Be Published
Title: Conformational plasticity of human acid-sensing ion channel 1a
Authors: Cahill J / Hartfield KA / Heusser SA / Ritter N / Poulsen MH / Yoshioka C / Pless SA / Baconguis I
History
DepositionOct 24, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47504.png

Downloads & links

-
Map

FileDownload / File: emd_47504.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of human ASIC1a at pH 7.5, Conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 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: 0.1
Minimum - Maximum-0.24652581 - 0.5368948
Average (Standard dev.)0.00035905774 (±0.011835091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 324.096 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_47504_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B corresponding to the primary map

Fileemd_47504_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)

-
Half map: Half map A corresponding to the primary map

Fileemd_47504_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)

-
Sample components

-
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

-
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)

-
Macromolecule #1: Acid-sensing ion channel 1

MacromoleculeName: Acid-sensing ion channel 1 / type: protein_or_peptide / ID: 1
Details: ...Details: GGRMELKAEEEEVGGVQPVSIQAFASSSTLHGLAHIFSYERLSLKRALWALCFLGSLAVLLCVCTERVQYYFHYHHVTKLDEVAASQLTFPAVTLCNLNEFRFSQVSKNDLYHAGELLALLNNRYEIPDTQMADEKQLEILQDKANFRSFKPKPFNMREFYDRAGHDIRDMLLSCHFRGEVCSAEDFKVVFTRYGKCYTFNSGRDGRPRLKTMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPFIDQLGFGVAPGFQTFVACQEQRLIYLPPPWGTCKAVTMDSDLDFFDSYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDQEYCVCEMPCNLTRYGKELSMVKIPSKASAKYLAKKFNKSEQYIGENILVLDIFFEVLNYETIEQKKAYEIAGLLGDIGGQMGLFIGASILTVLELFDYAYEVIKHKLCRRGKCQKEAKRSSADKGVALSLDDVKRHNPCESLRGHPAGMTYAANILPHHPARGTFEDFTC
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90111
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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