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- EMDB-34545: Structure of Xenopus tropicalis acid-sensitive outwardly rectifyi... -

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Basic information

Entry
Database: EMDB / ID: EMD-34545
TitleStructure of Xenopus tropicalis acid-sensitive outwardly rectifying channel ASOR (resting state)
Map data
Sample
  • Complex: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in GDN
    • Protein or peptide: Proton-activated chloride channel
KeywordsChloride Channel / MEMBRANE PROTEIN
Function / homologypH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / plasma membrane / Proton-activated chloride channel
Function and homology information
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsChi P / Wang X / Li J / Li K / Zhang Y / Geng J / Wu J / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: Cell Res / Year: 2024
Title: Molecular insights into the inhibition of proton-activated chloride channel by transfer RNA.
Authors: Pengliang Chi / Xiang Wang / Jialu Li / Hui Yang / Kaiju Li / Yuqi Zhang / Shiyi Lin / Leiye Yu / Shiqi Liu / Lu Chen / Ruobing Ren / Jianping Wu / Zhuo Huang / Jia Geng / Dong Deng /
History
DepositionOct 22, 2022-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34545.png

Downloads & links

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Map

FileDownload / File: emd_34545.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.0871.0871.087
CCP4 map header1.881.881.88
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.554
Minimum - Maximum-5.1831446 - 6.2324862
Average (Standard dev.)-0.0016256882 (±0.08057286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34545_half_map_1.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 : Complex of Xenopus tropical acid-sensitive outwardly rectifying c...

EntireName: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in GDN
Components
  • Complex: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in GDN
    • Protein or peptide: Proton-activated chloride channel

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Supramolecule #1: Complex of Xenopus tropical acid-sensitive outwardly rectifying c...

SupramoleculeName: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in GDN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)

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Macromolecule #1: Proton-activated chloride channel

MacromoleculeName: Proton-activated chloride channel / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 41.031789 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEAIRKELSR SYQELNEEAE PVAIDPEEAE DEEKEQEEAA SAVAPDRDSD RSSPPVRFSR TCLKNFFSVL LILVYLLLMG VAVFLVYQT ITDFRDKLKH PVMSVSYKEV NMYDAPGIAL YPGKARLLSC EHHWYDHIPP LKDPGQPGEN TCVTQDISYI D PYTNKTMK ...String:
MEAIRKELSR SYQELNEEAE PVAIDPEEAE DEEKEQEEAA SAVAPDRDSD RSSPPVRFSR TCLKNFFSVL LILVYLLLMG VAVFLVYQT ITDFRDKLKH PVMSVSYKEV NMYDAPGIAL YPGKARLLSC EHHWYDHIPP LKDPGQPGEN TCVTQDISYI D PYTNKTMK HALIVQGPRD VRRRELVFLQ FHLNETKQDF SAIDYLLFSS YEAFLKSHDQ VKFMQDCESS FSSWKFSGGF RT WVKMSLV KTKEEDGSQS VEFRQETSVV NFIDRRETPD KGDQLFFVVF EWKDPYIQEI QDIITANPWS MIALLCSVFL VLF KAADFA KLSVKWMIKV RRRHLKKRAR ELNHIS

UniProtKB: Proton-activated chloride channel

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172281
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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