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- PDB-9c07: Structure of K2P13.1 (THIK1) S136P in detergent -

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Basic information

Entry
Database: PDB / ID: 9c07
TitleStructure of K2P13.1 (THIK1) S136P in detergent
ComponentsPotassium channel subfamily K member 13
KeywordsTRANSPORT PROTEIN / Potassium channel / K2P channel
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
DODECANE / LINOLEIC ACID / HEXANE / : / N-OCTANE / HEXADECANE / Potassium channel subfamily K member 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsRoy-Chowdhury, S. / Adberemane-Ali, F. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01 MH093603 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure of the human K13.1 channel reveals a hydrophilic pore restriction and lipid cofactor site.
Authors: Shatabdi Roy-Chowdhury / Seil Jang / Fayal Abderemane-Ali / Fiona Naughton / Michael Grabe / Daniel L Minor /
Abstract: Polyunsaturated fatty acid (PUFA) lipids modulate the neuronal and microglial leak potassium channel K13.1 (THIK1) and other voltage-gated ion channel (VGIC) superfamily members through poorly ...Polyunsaturated fatty acid (PUFA) lipids modulate the neuronal and microglial leak potassium channel K13.1 (THIK1) and other voltage-gated ion channel (VGIC) superfamily members through poorly understood mechanisms. Here we present cryo-electron microscopy structures of human THIK1 and mutants, revealing a unique two-chamber aqueous inner cavity obstructed by a hydrophilic barrier important for gating, the flow restrictor, and a P1-M4 intersubunit interface lipid at a site, the PUFA site, corresponding to the K small-molecule modulator pocket. This overlap, together with functional studies, indicates that PUFA site lipids are THIK1 cofactors. Comparison with a PUFA-responsive VGIC, K7.1, reveals a shared modulatory role for the pore domain intersubunit interface, providing a framework for understanding PUFA action on the VGIC superfamily. Our findings reveal the distinct THIK1 architecture, highlight the importance of the P1-M4 interface for K control by natural and synthetic ligands and should aid in the development of THIK subfamily modulators for neuroinflammation and autism.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Potassium channel subfamily K member 13
A: Potassium channel subfamily K member 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,08038
Polymers78,7672
Non-polymers4,31236
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules UA

#1: Protein Potassium channel subfamily K member 13 / Tandem pore domain halothane-inhibited potassium channel 1 / THIK-1


Mass: 39383.613 Da / Num. of mol.: 2
Fragment: K2P13.1 (THIK1) residues 1 to 350 followed by SNS linker and 3c protease cleavage site
Mutation: N59Q. N65Q, S136P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK13 / Production host: Homo sapiens (human) / References: UniProt: Q9HB14

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Non-polymers , 6 types, 36 molecules

#2: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26
#3: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestY
Has protein modificationN

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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: homodimer of K2P13.1 (THIK1) S136P mutant / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
13cryoSPARC3.23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 508529 / Symmetry type: POINT

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