[English] 日本語
Yorodumi
- EMDB-83302: Cryo-EM structure of the outwardly rectifying potassium channel T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-83302
TitleCryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc
Map data
Sample
  • Complex: Cryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc
    • Protein or peptide: Outward-rectifier potassium channel TOK1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Keywordsion channel / K2P / two-pore-domain potassiumu channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


Tandem pore domain halothane-inhibited K+ channel (THIK) / Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / TWIK-releated acid-sensitive K+ channel (TASK) / TWIK-related spinal cord K+ channel (TRESK) / TWIK-related alkaline pH activated K+ channel (TALK) / TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / intracellular potassium ion homeostasis / potassium channel activity ...Tandem pore domain halothane-inhibited K+ channel (THIK) / Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / TWIK-releated acid-sensitive K+ channel (TASK) / TWIK-related spinal cord K+ channel (TRESK) / TWIK-related alkaline pH activated K+ channel (TALK) / TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / intracellular potassium ion homeostasis / potassium channel activity / voltage-gated potassium channel activity / cell periphery / plasma membrane
Similarity search - Function
Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Outward-rectifier potassium channel TOK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSano FK / Yamaguchi K / Hashimoto K / Sawada K / Hirano H / Itoh Y / Kise Y / Nureki O
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP26gm7110004 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627001 Japan
Japan Society for the Promotion of Science (JSPS)JP26K23281 Japan
Japan Society for the Promotion of Science (JSPS)JP23KJ0491 Japan
CitationJournal: To Be Published
Title: Structural basis of lipid-mediated gating in a two-pore domain potassium channel TOK1
Authors: Sano FK / Kasuya G / Yamaguchi K / Suzuki T / Hashimoto K / Inoue M / Sawada K / Ishitani R / Yoshimura K / Hirano H / Itoh Y / Nakajo K / Dohmae N / Kise Y / Nureki O
History
DepositionAug 30, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_83302.png

Downloads & links

-
Map

FileDownload / File: emd_83302.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 264 pix.
= 266.64 Å		1.01 Å/pix.
x 264 pix.
= 266.64 Å		1.01 Å/pix.
x 264 pix.
= 266.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.41376394 - 0.8908632
Average (Standard dev.)-0.0015744967 (±0.02488292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 266.63998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_83302_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_83302_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_83302_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_83302_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of the outwardly rectifying potassium channel T...

EntireName: Cryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc
Components
  • Complex: Cryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc
    • Protein or peptide: Outward-rectifier potassium channel TOK1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: POTASSIUM ION
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

-
Supramolecule #1: Cryo-EM structure of the outwardly rectifying potassium channel T...

SupramoleculeName: Cryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Outward-rectifier potassium channel TOK1

MacromoleculeName: Outward-rectifier potassium channel TOK1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.432695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSGTRFM NSFAKQTLGY GNMATVEQES SAQAVDSHSN NTPKQAKGVL AEELKDALR FRDERVSIIN AEPSSTLFVF WFVVSCYFPV ITACLGPVAN TISIACVVEK WRSLKNNSVV TNPRSNDTDV L MNQVKTVF ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSGTRFM NSFAKQTLGY GNMATVEQES SAQAVDSHSN NTPKQAKGVL AEELKDALR FRDERVSIIN AEPSSTLFVF WFVVSCYFPV ITACLGPVAN TISIACVVEK WRSLKNNSVV TNPRSNDTDV L MNQVKTVF DPPGIFAVNI ISLVLGFTSN IILMLHFSKK LTYLKSQLIN ITGWTIAGGM LLVDVIVCSL NDMPSIYSKT IG FWFACIS SGLYLVCTII LTIHFIGYKL GKYPPTFNLL PNERSIMAYT VLLSLWLIWG AGMFSGLLHI TYGNALYFCT VSL LTVGLG DILPKSVGAK IMVLIFSLSG VVLMGLIVFM TRSIIQKSSG PIFFFHRVEK GRSKSWKHYM DSSKNLSERE AFDL MKCIR QTASRKQHWF SLSVTIAIFM AFWLLGALVF KFAENWSYFN CIYFCFLCLL TIGYGDYAPR TGAGRAFFVI WALGA VPLM GAILSTVGDL LFDISTSLDI KIGESFNNKV KSIVFNGRQR ALSFMVNTGE IFEESDTADG DLEENTTSSQ SSQISE FND NNSEENDSGV TSPPASLQES FSSLSKASSP EGILPLEYVS SAEYALQDSG TCNLRNLQEL LKAVKKLHRI CLADKDY TL SFSDWSYIHK LHLRNITDIE EYTRGPEFWI SPDTPLKFPL NEPHFAFMML FKNIEELVGN LVEDEELYKV ISKRKFLG E HRKTLGGSGG SGPSRLEEEL RRRLTEPGSH HHHHHHH

UniProtKB: Outward-rectifier potassium channel TOK1

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 6 / 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: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #4: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 4 / Number of copies: 2 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 282434
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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