[English] 日本語
Yorodumi
- EMDB-51158: Structure of the human two pore domain potassium ion channel TASK... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51158
TitleStructure of the human two pore domain potassium ion channel TASK-3 (K2P9.1)
Map dataB factor sharpened map
Sample
  • Complex: K2P9.1 homodimer
    • Protein or peptide: Potassium channel subfamily K member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION
KeywordsK2P / membrane protein / potassium channel / ion channel
Function / homology
Function and homology information


negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / sodium channel activity / potassium ion import across plasma membrane ...negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / sodium channel activity / potassium ion import across plasma membrane / potassium channel activity / visual perception / potassium ion transport / synaptic vesicle / mitochondrial inner membrane / protein heterodimerization activity / dendrite / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsHall PH / Rodstrom KEJ / Tucker SJ
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T002018/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S008608/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W017741/1 United Kingdom
CitationJournal: Structure / Year: 2025
Title: Structures of TASK-1 and TASK-3 K2P channels provide insight into their gating and dysfunction in disease.
Authors: Peter Rory Hall / Thibault Jouen-Tachoire / Marcus Schewe / Peter Proks / Thomas Baukrowitz / Elisabeth P Carpenter / Simon Newstead / Karin E J Rödström / Stephen J Tucker /
Abstract: TASK-1 and TASK-3 are pH-sensitive two-pore domain (K2P/KCNK) K channels. Their functional roles make them promising targets for treatment of multiple disorders including sleep apnea, pain, and ...TASK-1 and TASK-3 are pH-sensitive two-pore domain (K2P/KCNK) K channels. Their functional roles make them promising targets for treatment of multiple disorders including sleep apnea, pain, and atrial fibrillation. Mutations in these channels are also associated with neurodevelopmental and hypertensive disorders. A previous crystal structure of TASK-1 revealed a lower "X-gate" as a hotspot for missense gain-of-function (GoF) mutations associated with DDSA (developmental delay with sleep apnea). However, the mechanisms of gating in TASK channels are still not fully understood. Here, we resolve structures for both human TASK-1 and TASK-3 by cryoelectron microscopy (cryo-EM), as well as a recurrent TASK-3 variant (G236R) associated with KCNK9 imprinting syndrome (KIS) (formerly known as Birk-Barel syndrome). Combined with functional studies of the X-gating mechanism, we provide evidence for how a highly conserved gating mechanism becomes defective in disease, and also provide further insight into the pathway of conformational changes that underlie the pH-dependent inhibition of TASK channel activity.
History
DepositionJul 25, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51158.png

Downloads & links

-
Map

FileDownload / File: emd_51158.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-1.0872562 - 1.6121852
Average (Standard dev.)0.0010252405 (±0.032363605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51158_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_51158_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_51158_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_51158_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : K2P9.1 homodimer

EntireName: K2P9.1 homodimer
Components
  • Complex: K2P9.1 homodimer
    • Protein or peptide: Potassium channel subfamily K member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION

-
Supramolecule #1: K2P9.1 homodimer

SupramoleculeName: K2P9.1 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Protein generated by removal of the 10xHis and FLAG purification tags with 3C protease cleavage
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 610 KDa

-
Macromolecule #1: Potassium channel subfamily K member 9

MacromoleculeName: Potassium channel subfamily K member 9 / type: protein_or_peptide / ID: 1
Details: M1 to D259, with a HRV 3C protease site. Fused purification tags were cleaved prior to EM sample preparation.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.308301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKRQNVRTLS LIVCTFTYLL VGAAVFDALE SDHEMREEEK LKAEEIRIKG KYNISSEDYR QLELVILQSE PHRAGVQWKF AGSFYFAIT VITTIGYGHA APGTDAGKAF CMFYAVLGIP LTLVMFQSLG ERMNTFVRYL LKRIKKCCGM RNTDVSMENM V TVGFFSCM ...String:
MKRQNVRTLS LIVCTFTYLL VGAAVFDALE SDHEMREEEK LKAEEIRIKG KYNISSEDYR QLELVILQSE PHRAGVQWKF AGSFYFAIT VITTIGYGHA APGTDAGKAF CMFYAVLGIP LTLVMFQSLG ERMNTFVRYL LKRIKKCCGM RNTDVSMENM V TVGFFSCM GTLCIGAAAF SQCEEWSFFH AYYYCFITLT TIGFGDYVAL QTKGALQKKP LYVAFSFMYI LVGLTVIGAF LN LVVLRFL TMNSEDERRD AEAELEVLFQ

UniProtKB: Potassium channel subfamily K member 9

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #3: POTASSIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 200 mM KCl, 0.12% w/v DM, 0.012% w/v CHS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Grid blotted for 3 seconds.
DetailsMonodisperse sample

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21363 / Average electron dose: 39.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 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

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 93760
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsAn initial model was built manually in COOT
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9g9v:
Structure of the human two pore domain potassium ion channel TASK-3 (K2P9.1)

+
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