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- PDB-7sk1: TWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 7sk1
TitleTWIK1 in MSP1E3D1 Lipid Nanodisc at pH 5.5
ComponentsPotassium channel subfamily K member 1
KeywordsTRANSPORT PROTEIN / K+ Channel / pH
Function / homology
Function and homology information


Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / inward rectifier potassium channel complex / ligand-gated channel activity / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / cellular response to acidic pH ...Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / inward rectifier potassium channel complex / ligand-gated channel activity / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / cellular response to acidic pH / glutamate secretion / sodium channel activity / potassium channel activity / potassium ion transmembrane transport / sodium ion transmembrane transport / chloride transmembrane transport / synaptic membrane / response to nicotine / brush border membrane / recycling endosome / perikaryon / endosome / apical plasma membrane / protein heterodimerization activity / dendrite / identical protein binding / membrane / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TWIK-1 / Two pore domain potassium channel, TWIK family / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TETRADECANE / : / N-OCTANE / Potassium channel subfamily K member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsTurney, T.S. / Brohawn, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123496 United States
Citation
Journal: Nat Commun / Year: 2022
Title: Structural Basis for pH-gating of the K channel TWIK1 at the selectivity filter.
Authors: Toby S Turney / Vivian Li / Stephen G Brohawn /
Abstract: TWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays ...TWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays unique properties among K2Ps including low basal activity and inhibition by extracellular protons through incompletely understood mechanisms. Here, we present cryo-EM structures of TWIK1 in lipid nanodiscs at high and low pH that reveal a previously undescribed gating mechanism at the K selectivity filter. At high pH, TWIK1 adopts an open conformation. At low pH, protonation of an extracellular histidine results in a cascade of conformational changes that close the channel by sealing the top of the selectivity filter, displacing the helical cap to block extracellular ion access pathways, and opening gaps for lipid block of the intracellular cavity. These data provide a mechanistic understanding for extracellular pH-gating of TWIK1 and illustrate how diverse mechanisms have evolved to gate the selectivity filter of K channels.
#1: Journal: Biorxiv / Year: 2021
Title: Structural Basis for pH-Gating of the K + Channel TWIK1 at the Selectivity Filter
Authors: Turney, T.S. / Li, V. / Brohawn, S.G.
History
DepositionOct 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_3d_fitting_list.accession_code ..._citation.journal_id_ISSN / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Potassium channel subfamily K member 1
B: Potassium channel subfamily K member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2749
Polymers76,5322
Non-polymers7437
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Potassium channel subfamily K member 1 / Inward rectifying potassium channel protein TWIK-1 / rTWIK / Potassium channel K2P1


Mass: 38265.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnk1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9Z2T2
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: TWIK1 in MSPE3D1 Lipid Nanodisc at pH 5.5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 5.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESC6H13NO4S1
2150 mMPotassium ChlorideKCl1
31 mMEDTAC10H16N2O81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50.3523 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1Topazparticle selection
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38126 / Symmetry type: POINT
Atomic model buildingB value: 143 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 3UKM

3ukm


Accession code: 3UKM / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084416
ELECTRON MICROSCOPYf_angle_d1.0695984
ELECTRON MICROSCOPYf_dihedral_angle_d15.285602
ELECTRON MICROSCOPYf_chiral_restr0.058668
ELECTRON MICROSCOPYf_plane_restr0.006728

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