45IM | pdb_000045im

Cryo-EM structure of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae in a lipid nanodisc

PDB DOI: https://doi.org/10.2210/pdb45IM/pdb
EM Map EMD-83302: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-08-30 Released: 2026-09-16
Deposition Author(s): Sano, F.K., Yamaguchi, K., Hashimoto, K., Sawada, K., Hirano, H., Itoh, Y., Kise, Y., Nureki, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 45IM

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of lipid-mediated gating in a two-pore domain potassium channel TOK1

Sano, F.K., 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.

To be published.

Macromolecule Content

Total Structure Weight: 173.46 kDa
Atom Count: 7,983
Modeled Residue Count: 964
Deposited Residue Count: 1,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outward-rectifier potassium channel TOK1	A, B	758	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TOK1, DUK1, YJL093C, J0911
UniProt
Find proteins for P40310 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40310 Go to UniProtKB: P40310
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40310
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN (Subject of Investigation/LOI) Query on LBN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
Y01 (Subject of Investigation/LOI) Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] K [auth B] L [auth B] C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP26gm7110004
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627001
Japan Society for the Promotion of Science (JSPS)	Japan	JP26K23281
Japan Society for the Promotion of Science (JSPS)	Japan	JP23KJ0491

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release