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- EMDB-36799: Human TWIK-related acid-sensitive potassium channel TASK3 at pH 6... -

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Basic information

Entry
Database: EMDB / ID: EMD-36799
TitleHuman TWIK-related acid-sensitive potassium channel TASK3 at pH 6.0, 5 mM KCl and 135 mM NaCl
Map data
Sample
  • Complex: CHS
    • Protein or peptide: Potassium channel subfamily K member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsAcid-sensitive / potassium ion channel / C-type / gating mechanism / MEMBRANE PROTEIN
Function / homology
Function and homology information


TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / potassium ion import across plasma membrane / potassium channel activity / potassium ion transmembrane transport / potassium ion transport / synaptic vesicle / plasma membrane
Similarity search - Function
Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsChen S / Lin H
Funding support China, 4 items
OrganizationGrant numberCountry
Other government20QA1405500
Other governmentXK2019006
Other governmentBX2021193
National Natural Science Foundation of China (NSFC)32301002 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: C-type inactivation and proton modulation mechanisms of the TASK3 channel.
Authors: Huajian Lin / Junnan Li / Qiansen Zhang / Huaiyu Yang / Shanshuang Chen /
Abstract: The TWIK-related acid-sensitive K channel 3 (TASK3) belongs to the two-pore domain (K2P) potassium channel family, which regulates cell excitability by mediating a constitutive "leak" potassium ...The TWIK-related acid-sensitive K channel 3 (TASK3) belongs to the two-pore domain (K2P) potassium channel family, which regulates cell excitability by mediating a constitutive "leak" potassium efflux in the nervous system. Extracellular acidification inhibits TASK3 channel, but the molecular mechanism by which channel inactivation is coupled to pH decrease remains unclear. Here, we report the cryo-electron microscopy structures of human TASK3 at neutral and acidic pH. Structural comparison revealed selectivity filter (SF) rearrangements upon acidification, characteristic of C-type inactivation, but with a unique structural basis. The extracellular mouth of the SF was prominently dilated and simultaneously blocked by a hydrophobic gate. His98 protonation shifted the conformational equilibrium between the conductive and C-type inactivated SF toward the latter by engaging a cation-π interaction with Trp78, consistent with molecular dynamics simulations and electrophysiological experiments. Our work illustrated how TASK3 is gated in response to extracellular pH change and implies how physiological stimuli might directly modulate the C-type gating of K2P channels.
History
DepositionJul 11, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36799.png

Downloads & links

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Map

FileDownload / File: emd_36799.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.9155574 - 4.101306
Average (Standard dev.)0.00058504916 (±0.078017466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36799_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36799_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : CHS

EntireName: CHS
Components
  • Complex: CHS
    • Protein or peptide: Potassium channel subfamily K member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: CHS

SupramoleculeName: CHS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium channel subfamily K member 9

MacromoleculeName: Potassium channel subfamily K member 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.173238 KDa
Recombinant expressionOrganism: eukaryotic plasmids (others)
SequenceString: MKRQNVRTLS LIVCTFTYLL VGAAVFDALE SDHEMREEEK LKAEEIRIKG KYNISSEDYR QLELVILQSE PHRAGVQWKF AGSFYFAIT VITTIGYGHA APGTDAGKAF CMFYAVLGIP LTLVMFQSLG ERMNTFVRYL LKRIKKCCGM RNTDVSMENM V TVGFFSCM ...String:
MKRQNVRTLS LIVCTFTYLL VGAAVFDALE SDHEMREEEK LKAEEIRIKG KYNISSEDYR QLELVILQSE PHRAGVQWKF AGSFYFAIT VITTIGYGHA APGTDAGKAF CMFYAVLGIP LTLVMFQSLG ERMNTFVRYL LKRIKKCCGM RNTDVSMENM V TVGFFSCM GTLCIGAAAF SQCEEWSFFH AYYYCFITLT TIGFGDYVAL QTKGALQKKP LYVAFSFMYI LVGLTVIGAF LN LVVLRFL TMNSEDERRD AENLYFQGVD AGLEVLFQ

UniProtKB: Potassium channel subfamily K member 9

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationFormulaName
5.0 mMKClpotassium chloride
30.0 mMC6H15N3O3Bis-Tris
135.0 mMNaClsodium chloride
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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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: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 291294
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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