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- PDB-45ir: Cryo-EM structure of the T322I mutant of the outwardly rectifying... -

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Basic information

Entry
Database: PDB / ID: 45ir
TitleCryo-EM structure of the T322I mutant of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae
ComponentsOutward-rectifier potassium channel TOK1
KeywordsMEMBRANE PROTEIN / K2P
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
: / CHOLESTEROL HEMISUCCINATE / Outward-rectifier potassium channel TOK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsSano, F.K. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP26gm7110004 Japan
CitationJournal: To Be Published
Title: Structural basis of lipid-mediated gating in a two-pore domain potassium channel TOK1
Authors: Sano, F.K. / Nureki, O.
History
DepositionAug 30, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outward-rectifier potassium channel TOK1
B: Outward-rectifier potassium channel TOK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,9807
Polymers168,8902
Non-polymers1,0915
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Outward-rectifier potassium channel TOK1 / Two-domain outward rectifier K(+) channel YORK


Mass: 84444.750 Da / Num. of mol.: 2 / Mutation: T322I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOK1, DUK1, YJL093C, J0911 / Production host: Homo sapiens (human) / References: UniProt: P40310
#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the T322I mutant of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163368 / Symmetry type: POINT
RefinementHighest resolution: 2.91 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027938
ELECTRON MICROSCOPYf_angle_d0.44810770
ELECTRON MICROSCOPYf_dihedral_angle_d41068
ELECTRON MICROSCOPYf_chiral_restr0.041248
ELECTRON MICROSCOPYf_plane_restr0.0031282

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