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- EMDB-48216: Structure of the human TWIK-2 potassium channel -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48216
TitleStructure of the human TWIK-2 potassium channel
Map dataCryo-EM map of TWIK2-apo
Sample
  • Complex: TWIK-2
    • Protein or peptide: Potassium channel subfamily K member 6
  • Ligand: POTASSIUM ION
  • Ligand: HEPTANE
KeywordsTwo-pore potassium channel K2P6 TWIK2 K2P channel / MEMBRANE PROTEIN
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
Potassium channel subfamily K member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsKhanra NK / Long SB
Funding support United States, 1 items
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 NK / Wang C / Delgado B / Long SB
History
DepositionDec 6, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48216.png

Downloads & links

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Map

FileDownload / File: emd_48216.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of TWIK2-apo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.74849 - 4.6240845
Average (Standard dev.)-0.0009074726 (±0.061563596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 278.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of TWIK2-apo

Fileemd_48216_half_map_1.map
AnnotationHalf map A of TWIK2-apo
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of TWIK2-apo

Fileemd_48216_half_map_2.map
AnnotationHalf map B of TWIK2-apo
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TWIK-2

EntireName: TWIK-2
Components
  • Complex: TWIK-2
    • Protein or peptide: Potassium channel subfamily K member 6
  • Ligand: POTASSIUM ION
  • Ligand: HEPTANE

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Supramolecule #1: TWIK-2

SupramoleculeName: TWIK-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: human TWIK-2 potassium channel
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.74728 KDa

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Macromolecule #1: Potassium channel subfamily K member 6

MacromoleculeName: Potassium channel subfamily K member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.775113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRGALLAGA LAAYAAYLVL GALLVARLEG PHEARLRAEL ETLRAQLLQR SPCVAAPALD AFVERVLAAG RLGRVVLANA SGSANASDP AWDFASALFF ASTLITTVGY GYTTPLTDAG KAFSIAFALL GVPTTMLLLT ASAQRLSLLL THVPLSWLSM R WGWDPRRA ...String:
MRRGALLAGA LAAYAAYLVL GALLVARLEG PHEARLRAEL ETLRAQLLQR SPCVAAPALD AFVERVLAAG RLGRVVLANA SGSANASDP AWDFASALFF ASTLITTVGY GYTTPLTDAG KAFSIAFALL GVPTTMLLLT ASAQRLSLLL THVPLSWLSM R WGWDPRRA ACWHLVALLG VVVTVCFLVP AVIFAHLEEA WSFLDAFYFC FISLSTIGLG DYVPGEAPGQ PYRALYKVLV TV YLFLGLV AMVLVLQTFR HVSDLHGLTE LILLPPPCPA SFNADEDDRV DILGPQPESH QQLSASSHTD YASIPR

UniProtKB: Potassium channel subfamily K member 6

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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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

Concentration6.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMKClPotassium Chloride
0.0025 %LMNG2,2-didecylpropane-1,3-bis-beta-D-maltopyranoside
0.00025 %CHSCholesteryl Hemisuccinate
0.000825 %GDNglyco-diosgenin

Details: 20 mM HEPES, 150 mM KCl, pH 7.5, 0.0025 % LMNG, 0.00025 % CHS, 0.000825 % GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5 uL sample, blot time = 3.0 sec, blot force = 0.
DetailsMonodisperse recombinantly purified TWIK2

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22020573
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 89.3
Output model

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

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