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- EMDB-61467: Cryo-EM Structure of Human Kcnk13. -

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Basic information

Entry
Database: EMDB / ID: EMD-61467
TitleCryo-EM Structure of Human Kcnk13.
Map data
Sample
  • Complex: Wild type K2P ion channel
    • 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: ARACHIDONIC ACID
  • Ligand: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM ION
Keywordspotassium channel / microglia function / K2P family / 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 / metal ion binding / identical protein 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: 2.74 Å
AuthorsBaobin L / Ran Z / Jin W
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_61467.png

Downloads & links

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Map

FileDownload / File: emd_61467.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: 0.3
Minimum - Maximum-1.2355496 - 2.3490593
Average (Standard dev.)0.0015422842 (±0.058529943)
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_61467_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_61467_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Wild type K2P ion channel

EntireName: Wild type K2P ion channel
Components
  • Complex: Wild type K2P ion channel
    • 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: ARACHIDONIC ACID
  • Ligand: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • Ligand: POTASSIUM ION

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Supramolecule #1: Wild type K2P ion channel

SupramoleculeName: Wild type K2P ion channel / 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: 44.027766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGHLNEDNA RFLLLAALIV LYLLGGAAVF SALELAHERQ AKQRWEERLA NFSRGHNLSR DELRGFLRHY EEATRAGIRV DNVRPRWDF TGAFYFVGTV VSTIGFGMTT PATVGGKIFL IFYGLVGCSS TILFFNLFLE RLITIIAYIM KSCHQRQLRR R GALPQESL ...String:
GPGHLNEDNA RFLLLAALIV LYLLGGAAVF SALELAHERQ AKQRWEERLA NFSRGHNLSR DELRGFLRHY EEATRAGIRV DNVRPRWDF TGAFYFVGTV VSTIGFGMTT PATVGGKIFL IFYGLVGCSS TILFFNLFLE RLITIIAYIM KSCHQRQLRR R GALPQESL KDAGQCEVDS LAGWKPSVYY VMLILCTASI LISCCASAMY TPIEGWSYFD SLYFCFVAFS TIGFGDLVSS QN AHYESQG LYRFANFVFI LMGVCCIYSL FNVISILIKQ SLNWILRKMD SGCCPQCQRG LLRSRRNVVM PGSVRNRCNI SIE TDGVAE SDTDGRRLSG EMISMKDLLA ANKASLAILQ KQLSEMANGC PHQTSTLARD NEFSGGVGAF AIMNNRLAE

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: 12 / 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: ARACHIDONIC ACID

MacromoleculeName: ARACHIDONIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: ACD
Molecular weightTheoretical: 304.467 Da
Chemical component information

ChemComp-ACD:
ARACHIDONIC ACID

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Macromolecule #5: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec...

MacromoleculeName: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 2 / Formula: D21
Molecular weightTheoretical: 674.929 Da
Chemical component information

ChemComp-D21:
(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 4 / 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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
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: Tecnai Spirit / 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237767
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9jgz:
Cryo-EM Structure of Human Kcnk13.

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