9JGZ | pdb_00009jgz

Cryo-EM Structure of Human Kcnk13.

PDB DOI: https://doi.org/10.2210/pdb9JGZ/pdb
EM Map EMD-61467: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2024-09-08 Released: 2025-05-07
Deposition Author(s): Baobin, L., Ran, Z., Jin, W.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Ministry of Education (MoE, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Gating mechanism of the two-pore-domain potassium channel THIK1.

Fang, X., Jin, H., Wang, J., Zhang, R., Li, B.

(2025) Nat Struct Mol Biol 32: 1175-1182

PubMed: 40307591 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-025-01542-4
Primary Citation of Related Structures:
9JGZ, 9JH1

PubMed 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 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.

Organizational Affiliation

Department of Anesthesiology, Fudan University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 99.85 kDa
Atom Count: 4,904
Modeled Residue Count: 574
Deposited Residue Count: 790
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel subfamily K member 13	A, B	395	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HB14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	C [auth A] D [auth A] H [auth A] I [auth A] J [auth A] C [auth A], D [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth B], V [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth B] Focus chain V [auth B]
D21 Query on D21 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B]	G [auth A], T [auth B]	(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate C₃₇ H₇₁ O₈ P OPVZUEPSMJNLOM-PGUFJCEWSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]
ACD (Subject of Investigation/LOI) Query on ACD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth B] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B]	F [auth A], S [auth B]	ARACHIDONIC ACID C₂₀ H₃₂ O₂ YZXBAPSDXZZRGB-DOFZRALJSA-N		Interactions Focus chain F [auth A] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain S [auth B]
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B]	E [auth A], R [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain E [auth A] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain R [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	L [auth A], M [auth A], W [auth B], X [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Baobin, L.

Ran, Z.

Jin, W.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	STI2030-Major Projects-2022ZD0207800
National Natural Science Foundation of China (NSFC)	China	32371261
National Natural Science Foundation of China (NSFC)	China	32301011
Ministry of Education (MoE, China)	China	2632024ZD10