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- PDB-8k1q: Human TWIK-related acid-sensitive potassium channel TASK3 at pH 6... -

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Basic information

Entry
Database: PDB / ID: 8k1q
TitleHuman TWIK-related acid-sensitive potassium channel TASK3 at pH 6.0, 5 mM KCl and 135 mM NaCl
ComponentsPotassium channel subfamily K member 9
KeywordsMEMBRANE PROTEIN / Acid-sensitive / potassium ion channel / C-type / gating mechanism
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
: / CHOLESTEROL HEMISUCCINATE / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsChen, S. / Lin, H.
Funding support China, 4items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel subfamily K member 9
B: Potassium channel subfamily K member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34510
Polymers62,3462
Non-polymers2,9998
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Potassium channel subfamily K member 9 / Acid-sensitive potassium channel protein TASK-3 / TWIK-related acid-sensitive K(+) channel 3 / Two ...Acid-sensitive potassium channel protein TASK-3 / TWIK-related acid-sensitive K(+) channel 3 / Two pore potassium channel KT3.2 / Two pore K(+) channel KT3.2


Mass: 31173.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK9, TASK3 / Production host: eukaryotic plasmids (others) / References: UniProt: Q9NPC2
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CHS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: eukaryotic plasmids (others)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMpotassium chlorideKCl1
230 mMBis-TrisC6H15N3O31
3135 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291294 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0014156
ELECTRON MICROSCOPYf_angle_d0.3285644
ELECTRON MICROSCOPYf_dihedral_angle_d6.602604
ELECTRON MICROSCOPYf_chiral_restr0.031650
ELECTRON MICROSCOPYf_plane_restr0.001664

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