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- PDB-9mek: Structure of the human TWIK-2 potassium channel -

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Basic information

Entry
Database: PDB / ID: 9mek
TitleStructure of the human TWIK-2 potassium channel
ComponentsPotassium channel subfamily K member 6
KeywordsMEMBRANE PROTEIN / Two-pore potassium channel K2P6 TWIK2 K2P channel
Function / homology
Function and homology information


regulation of lysosome size / Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / outward rectifier potassium channel activity / negative regulation of systemic arterial blood pressure / positive regulation of NLRP3 inflammasome complex assembly / potassium channel activity ...regulation of lysosome size / Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / inward rectifier potassium channel activity / outward rectifier potassium channel activity / negative regulation of systemic arterial blood pressure / positive regulation of NLRP3 inflammasome complex assembly / potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / potassium ion transport / late endosome membrane / lysosomal membrane / metal ion binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TWIK-2 / Two pore domain potassium channel, TWIK family / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
HEPTANE / : / Potassium channel subfamily K member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsKhanra, N.K. / Long, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131921 United States
CitationJournal: To Be Published
Title: Structure of the human TWIK-2 potassium channel and its inhibition by pimozide
Authors: Khanra, N.K. / Wang, C. / Delgado, B. / Long, S.B.
History
DepositionDec 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel subfamily K member 6
B: Potassium channel subfamily K member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9078
Polymers67,5502
Non-polymers3576
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Potassium channel subfamily K member 6 / Inward rectifying potassium channel protein TWIK-2 / TWIK-originated similarity sequence


Mass: 33775.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK6, TOSS, TWIK2 / Production host: Homo sapiens (human) / References: UniProt: Q9Y257
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16 / 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: TWIK-2 / Type: COMPLEX / Details: human TWIK-2 potassium channel / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.03374728 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Details: 20 mM HEPES, 150 mM KCl, pH 7.5, 0.0025 % LMNG, 0.00025 % CHS, 0.000825 % GDN
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
2150 mMPotassium ChlorideKCl1
30.0025 %2,2-didecylpropane-1,3-bis-beta-D-maltopyranosideLMNG1
40.00025 %Cholesteryl HemisuccinateCHS1
50.000825 %glyco-diosgeninGDN1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse recombinantly purified TWIK2
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K / Details: 3.5 uL sample, blot time = 3.0 sec, blot force = 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60.76 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
2EPU3.8image acquisition
4cryoSPARCv4.5.0CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22020573
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131053 / Symmetry type: POINT
Atomic model buildingB value: 89.3

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