45IP | pdb_000045ip

Cryo-EM structure of the R323A mutant (ICD-ordered class) of the outwardly rectifying potassium channel TOK1 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb45IP/pdb
EM Map EMD-83305: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2026-08-30 Released: 2026-09-16
Deposition Author(s): Sano, F.K., Nureki, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 45IP

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., Nureki, O.

To be published.

Macromolecule Content

Total Structure Weight: 174.05 kDa
Atom Count: 8,085
Modeled Residue Count: 978
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): 1 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 F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	F [auth A], G [auth A], O [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B]
Y01 (Subject of Investigation/LOI) Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] L [auth B] M [auth B] C [auth A], D [auth A], E [auth A], L [auth B], M [auth B], N [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 L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.22 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

Revision History (Full details and data files)

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