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- EMDB-22343: Cryo-EM structure of a proton-activated chloride channel -

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Basic information

Entry
Database: EMDB / ID: EMD-22343
TitleCryo-EM structure of a proton-activated chloride channel
Map dataCryo-EM structure of a proton-activated chloride channel
Sample
  • Complex: TMEM206
    • Protein or peptide: Proton-activated chloride channel
Keywordsion channel / TRANSPORT PROTEIN
Function / homologyTMEM206 protein / TMEM206 protein family / plasma membrane / Proton-activated chloride channel
Function and homology information
Biological speciesTakifugu rubripes (torafugu) / Takifugu bimaculatus (fish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsDeng Z / Zhang J / Yuan P
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of a proton-activated chloride channel TMEM206.
Authors: Zengqin Deng / Yonghui Zhao / Jing Feng / Jingying Zhang / Haiyan Zhao / Michael J Rau / James A J Fitzpatrick / Hongzhen Hu / Peng Yuan /
Abstract: TMEM206 has been recently identified as an evolutionarily conserved chloride channel that underlies ubiquitously expressed, proton-activated, outwardly rectifying anion currents. Here, we report the ...TMEM206 has been recently identified as an evolutionarily conserved chloride channel that underlies ubiquitously expressed, proton-activated, outwardly rectifying anion currents. Here, we report the cryo-electron microscopy structure of pufferfish TMEM206, which forms a trimeric channel, with each subunit comprising two transmembrane segments and a large extracellular domain. An ample vestibule in the extracellular region is accessible laterally from the three side portals. The central pore contains multiple constrictions. A conserved lysine residue near the cytoplasmic end of the inner helix forms the presumed chloride ion selectivity filter. Unprecedentedly, the core structure and assembly closely resemble those of the epithelial sodium channel/degenerin family of sodium channels that are unrelated in amino acid sequence and conduct cations instead of anions. Together with electrophysiology, this work provides insights into ion conduction and gating for a new class of chloride channels that is architecturally distinct from previously characterized chloride channel families.
History
DepositionJul 22, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ji3
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22343.png

Downloads & links

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Map

FileDownload / File: emd_22343.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a proton-activated chloride channel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.015 / Movie #1: 0.018
Minimum - Maximum-0.033527434 - 0.068844594
Average (Standard dev.)-0.000024337776 (±0.0022724776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 242.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z242.000242.000242.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0340.069-0.000

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Supplemental data

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Sample components

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Entire : TMEM206

EntireName: TMEM206
Components
  • Complex: TMEM206
    • Protein or peptide: Proton-activated chloride channel

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Supramolecule #1: TMEM206

SupramoleculeName: TMEM206 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Takifugu rubripes (torafugu)

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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: Takifugu bimaculatus (fish)
Molecular weightTheoretical: 52.907641 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MRRNSYREFI DEDDEDDGNK DVPNCFDDVI DSPEEVEPND SASPDDDNRQ ESSRSRRFSK LCVKNVFTVL LILIYLLLTA LAAFLAYQT ISEVLEKLKN PVMSVTYQEV DSFPRPGIAL YPGNAQLLSC SHYYHNDIPP VVEPGRPQEI DCVVTEVTYV G PFSSQGEK ...String:
MRRNSYREFI DEDDEDDGNK DVPNCFDDVI DSPEEVEPND SASPDDDNRQ ESSRSRRFSK LCVKNVFTVL LILIYLLLTA LAAFLAYQT ISEVLEKLKN PVMSVTYQEV DSFPRPGIAL YPGNAQLLSC SHYYHNDIPP VVEPGRPQEI DCVVTEVTYV G PFSSQGEK RALVVRGPSE VRSKEMVFMQ FSSNETGEDF SAISYMIFAD FTDLIDSQNK SRFMGECETN CSRWTFSGGF RT WVKMSLV KTFGKQNDSV EFRQESAVVK FNDRRPAAEQ INQLYFAVFQ WRDPYIQQNK MIVTANPWSS IAILSGVFMA LFK AANFAK LTIQWIIRMR KRHLRNKERE LKQADLEDNW ETLNDNLKVI EKADNAAQVK DALTKMRAAA LDAQKATPPK LEDK SPDSP EMKDFRHGFD ILVGQIDDAL KLANEGKVKE AQAAAEQLKT TRNAYIQKYL SNSLEVLF

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 62.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 505115
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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