9BYI | pdb_00009byi

Structure of human K2P13.1 (THIK1) in detergent

• PDB DOI: https://doi.org/10.2210/pdb9BYI/pdb
• EM Map EMD-45034: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-05-23 Released: 2025-02-26 
• Deposition Author(s): Roy-Chowdhury, S., Minor, D.L.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the human K 2P 13.1 channel reveals a hydrophilic pore restriction and lipid cofactor site.

Roy-Chowdhury, S., Jang, S., Abderemane-Ali, F., Naughton, F., Grabe, M., Minor Jr., D.L.

(2025) Nat Struct Mol Biol 32: 1154-1166

• PubMed: 40011746 
• DOI: https://doi.org/10.1038/s41594-024-01476-3
• Primary Citation Related Structures: 
  9BSN, 9BWS, 9BYI, 9C07, 9C09


• PubMed Abstract: 
  

  Polyunsaturated fatty acid (PUFA) lipids modulate the neuronal and microglial leak potassium channel K _2P 13.1 (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 _2P small-molecule modulator pocket. This overlap, together with functional studies, indicates that PUFA site lipids are THIK1 cofactors. Comparison with a PUFA-responsive VGIC, K _v 7.1, 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 _2P control by natural and synthetic ligands and should aid in the development of THIK subfamily modulators for neuroinflammation and autism.

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Organizational Affiliation: 
• Cardiovascular Research Institute, UCSF Medical Center, San Francisco, CA, USA.
Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
Cardiovascular Research Institute, UCSF Medical Center, San Francisco, CA, USA. [e-mail].
Departments of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 82.96 kDa 
• Atom Count: 4,505 
• Modeled Residue Count: 524 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel subfamily K member 13	A [auth U], B [auth A]	350	Homo sapiens	Mutation(s): 2  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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EIC (Subject of Investigation/LOI)	CA [auth A], O [auth U]	LINOLEIC ACID C18 H32 O2 OYHQOLUKZRVURQ-HZJYTTRNSA-N
R16	G [auth U], T [auth A]	HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N
D12	D [auth U], DA [auth A], L [auth U], M [auth U], P [auth U], Q [auth A], Y [auth A], Z [auth A]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
OCT	BA [auth A], F [auth U], H [auth U], I [auth U], J [auth U], K [auth U], N [auth U], S [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX	AA [auth A], C [auth U], E [auth U], R [auth A]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
K	EA [auth A], FA [auth A], GA [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Roy-Chowdhury, S., Minor, D.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01 MH093603

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2025-03-12
  Changes: Data collection, Database references
• Version 1.2: 2025-05-21
  Changes: Data collection
• Version 1.3: 2025-07-30
  Changes: Data collection, Database references