[English] 日本語
Yorodumi
- EMDB-47258: hTHIK1 Cryo-EM structure in GDN detergent -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47258
TitlehTHIK1 Cryo-EM structure in GDN detergent
Map data
Sample
  • Complex: THIK1 ion channel dimer
    • Protein or peptide: Potassium channel subfamily K member 13
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsKCNK13 (THIK1) K2P ion channel dimer / CHS/GDN detergent / HEK293GnTi- / 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: 3.2 Å
AuthorsRiel EB / Riegelhaupt PM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM145918 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K08-GM132781 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The cryo-EM structure and physical basis for anesthetic inhibition of the THIK1 K2P channel.
Authors: Elena B Riel / Weiming Bu / Thomas T Joseph / Leila Khajoueinejad / Roderic G Eckenhoff / Paul M Riegelhaupt /
Abstract: THIK1 tandem pore domain (K2P) potassium channels regulate microglial surveillance of the central nervous system and responsiveness to inflammatory insults. With microglia recognized as critical to ...THIK1 tandem pore domain (K2P) potassium channels regulate microglial surveillance of the central nervous system and responsiveness to inflammatory insults. With microglia recognized as critical to the pathogenesis of neurodegenerative diseases, THIK1 channels are putative therapeutic targets to control microglia dysfunction. While THIK channels can principally be distinguished from other K2Ps by their distinctive inhibitory response to volatile anesthetics (VAs), molecular details governing THIK channel gating remain largely unexplored. Here, we report a 3.2 Å cryo-electron microscopy structure of the THIK1 channel in a closed conformation. A central pore gate located directly below the THIK1 selectivity filter is formed by inward-facing TM4 helix tyrosine residues that occlude the ion conduction pathway. VA inhibition of THIK requires closure of this central pore gate. Using a combination of anesthetic photolabeling, electrophysiology, and molecular dynamics simulation, we identify a functionally critical THIK1 VA binding site positioned between the central gate and a structured section of the THIK1 TM2/TM3 loop. Our results demonstrate the molecular architecture of the THIK1 channel and elucidate critical structural features involved in regulation of THIK1 channel gating and anesthetic inhibition.
History
DepositionOct 9, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47258.png

Downloads & links

-
Map

FileDownload / File: emd_47258.map.gz / Format: CCP4 / Size: 56.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 246 pix.
= 196.274 Å		0.8 Å/pix.
x 246 pix.
= 196.274 Å		0.8 Å/pix.
x 246 pix.
= 196.274 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79786 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.17662638 - 0.24678269
Average (Standard dev.)0.0000021164365 (±0.0056880126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 196.27405 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_47258_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_47258_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47258_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : THIK1 ion channel dimer

EntireName: THIK1 ion channel dimer
Components
  • Complex: THIK1 ion channel dimer
    • Protein or peptide: Potassium channel subfamily K member 13
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: POTASSIUM ION
  • Ligand: water

-
Supramolecule #1: THIK1 ion channel dimer

SupramoleculeName: THIK1 ion channel dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: C-terminally truncated THIK1 ion channel dimer
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Potassium channel subfamily K member 13

MacromoleculeName: Potassium channel subfamily K member 13 / type: protein_or_peptide / ID: 1 / Details: C-terminal truncation after residue S309 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.818398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGRGFSWGP GHLNEDNARF LLLAALIVLY LLGGAAVFSA LELAHERQAK QRWEERLANF SRGHNLSRDE LRGFLRHYEE ATRAGIRVD NVRPRWDFTG AFYFVGTVVS TIGFGMTTPA TVGGKIFLIF YGLVGCSSTI LFFNLFLERL ITIIAYIMKS C HQRQLRRR ...String:
MAGRGFSWGP GHLNEDNARF LLLAALIVLY LLGGAAVFSA LELAHERQAK QRWEERLANF SRGHNLSRDE LRGFLRHYEE ATRAGIRVD NVRPRWDFTG AFYFVGTVVS TIGFGMTTPA TVGGKIFLIF YGLVGCSSTI LFFNLFLERL ITIIAYIMKS C HQRQLRRR GALPQESLKD AGQCEVDSLA GWKPSVYYVM LILCTASILI SCCASAMYTP IEGWSYFDSL YFCFVAFSTI GF GDLVSSQ NAHYESQGLY RFANFVFILM GVCCIYSLFN VISILIKQSL NWILRKMDSG CCPQCQRGLL RS

UniProtKB: Potassium channel subfamily K member 13

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMKClpotassium chloride
20.0 mMTrisTris
0.01 %GDNglyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 14246 / Average electron dose: 48.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware: (Name: RELION (ver. 3.1.2), CTFFIND (ver. 4.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Initial model created with Relion 3.1.2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168294
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more