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- EMDB-61469: The Cryo-EM structure of Kcnk13-S136P -

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Basic information

Entry
Database: EMDB / ID: EMD-61469
TitleThe Cryo-EM structure of Kcnk13-S136P
Map data
Sample
  • Complex: Homo dimeric of K2P-S136P.
    • Protein or peptide: Potassium channel subfamily K member 13
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: LINOLEIC ACID
  • Ligand: POTASSIUM ION
Keywordspotassium channel / microglia function / cryo-EM structure / neurodegenerative diseases / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of excitatory synapse pruning / Tandem pore domain halothane-inhibited K+ channel (THIK) / regulation of NLRP3 inflammasome complex assembly / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport ...regulation of excitatory synapse pruning / Tandem pore domain halothane-inhibited K+ channel (THIK) / regulation of NLRP3 inflammasome complex assembly / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / protein heterodimerization activity / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, THIK / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily K member 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsXinagyun F / Haichao J / Jin W / Ran Z / Baobin L
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)STI2030-Major Projects-2022ZD0207800 China
National Natural Science Foundation of China (NSFC)32371261 China
National Natural Science Foundation of China (NSFC)32301011 China
Ministry of Education (MoE, China)2632024ZD10 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Gating mechanism of the two-pore-domain potassium channel THIK1.
Authors: Xiangyun Fang / Haichao Jin / Jin Wang / Ran Zhang / Baobin Li /
Abstract: TWIK-related halothane-inhibited potassium channel (THIK1) maintains the resting membrane potential and regulates potassium efflux in microglia. It is a potential therapeutic target for ...TWIK-related halothane-inhibited potassium channel (THIK1) maintains the resting membrane potential and regulates potassium efflux in microglia. It is a potential therapeutic target for neurodegenerative disorders, neuropathic pain and inflammation. However, the mechanism underlying its function remains unclear. Here we used cryo-electron microscopy to solve the structures of full-length human THIK1, revealing two inner gates and a C-type selectivity filter gate, distinct from other two-pore-domain potassium channels. One inner gate, formed by a short helix in the distal C terminus, introduces a unique gating mechanism involving the distal cytoplasmic domain. The other, beneath the selectivity filter, is constricted by Y273 in the M4 helix, dividing the cavity. In addition, the selectivity filter gate is modulated by polyunsaturated fatty acids. These structural insights into THIK1 gating, through the distal C-terminal helices, hydrophilic residues and selectivity filter, advance our understanding of THIK1's role in microglial homeostasis and neuropathologies.
History
DepositionSep 8, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61469.png

Downloads & links

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Map

FileDownload / File: emd_61469.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.68 Å		0.93 Å/pix.
x 240 pix.
= 223.68 Å		0.93 Å/pix.
x 240 pix.
= 223.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.358
Minimum - Maximum-0.88223755 - 1.6020467
Average (Standard dev.)0.00018511589 (±0.04196212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61469_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61469_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo dimeric of K2P-S136P.

EntireName: Homo dimeric of K2P-S136P.
Components
  • Complex: Homo dimeric of K2P-S136P.
    • Protein or peptide: Potassium channel subfamily K member 13
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: LINOLEIC ACID
  • Ligand: POTASSIUM ION

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Supramolecule #1: Homo dimeric of K2P-S136P.

SupramoleculeName: Homo dimeric of K2P-S136P. / 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 13

MacromoleculeName: Potassium channel subfamily K member 13 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.955248 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARFLLLAALI VLYLLGGAAV FSALELAHER QAKQRWEERL ANFSRGHNLS RDELRGFLRH YEEATRAGIR VDNVRPRWDF TGAFYFVGT VVSTIGFGMT TPATVGGKIF LIFYGLVGCP STILFFNLFL ERLITIIAYI MKSCHQRQLR RRGALPQESL K DAGQCEVD ...String:
ARFLLLAALI VLYLLGGAAV FSALELAHER QAKQRWEERL ANFSRGHNLS RDELRGFLRH YEEATRAGIR VDNVRPRWDF TGAFYFVGT VVSTIGFGMT TPATVGGKIF LIFYGLVGCP STILFFNLFL ERLITIIAYI MKSCHQRQLR RRGALPQESL K DAGQCEVD SLAGWKPSVY YVMLILCTAS ILISCCASAM YTPIEGWSYF DSLYFCFVAF STIGFGDLVS SQNAHYESQG LY RFANFVF ILMGVCCIYS LFNVISILIK QSLNWILRKM DSGCCP

UniProtKB: Potassium channel subfamily K member 13

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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Macromolecule #4: POTASSIUM ION

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81279
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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