9FT7 | pdb_00009ft7

Structure of the human two pore domain potassium ion channel THIK-1 (K2P13.1) in a closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the human THIK-1 K2P K + channel reveals a lower Y gate regulated by lipids and anesthetics.

Rodstrom, K.E.J.Eymsh, B.Proks, P.Hayre, M.S.Cordeiro, S.Mendez-Otalvaro, E.Madry, C.Rowland, A.Kopec, W.Newstead, S.Baukrowitz, T.Schewe, M.Tucker, S.J.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01497-6
  • Primary Citation of Related Structures:  
    9FT7

  • PubMed Abstract: 

    THIK-1 (KCNK13) is a halothane-inhibited and anionic-lipid-activated two-pore domain (K2P) K + channel implicated in microglial activation and neuroinflammation, and a current target for the treatment of neurodegenerative disorders, for example Alzheimer's disease and amyothropic lateral sclerosis (ALS). However, compared to other K2P channels, little is known about the structural and functional properties of THIK-1. Here we present a 3.16-Å-resolution cryo-EM structure of human THIK-1 that reveals several distinct features, in particular, a tyrosine in M4 that contributes to a lower 'Y gate' that opens upon activation by physiologically relevant G-protein-coupled receptor and lipid signaling pathways. We demonstrate that linoleic acid bound within a modulatory pocket adjacent to the filter influences channel activity, and that halothane inhibition involves a binding site within the inner cavity, both resulting in conformational changes to the Y gate. Finally, the extracellular cap domain contains positively charged residues that line the ion exit pathway and contribute to the distinct biophysical properties of this channel. Overall, our results provide structural insights into THIK-1 function and identify distinct regulatory sites that expand its potential as a drug target for the modulation of microglial function.


  • Organizational Affiliation

    Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium channel subfamily K member 13
A, B
298Homo sapiensMutation(s): 0 
Gene Names: KCNK13
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB14 (Homo sapiens)
Explore Q9HB14 
Go to UniProtKB:  Q9HB14
GTEx:  ENSG00000152315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HB14
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T002018/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S008608/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/W017741/1
Wellcome TrustUnited KingdomWT084655MA
Wellcome TrustUnited Kingdom102161/B/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release