9DI8 | pdb_00009di8

Ca2+ bound aplysia Slo1 - R196Q

PDB DOI: https://doi.org/10.2210/pdb9DI8/pdb
EM Map EMD-46901: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Aplysia californica
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-09-05 Released: 2025-06-18
Deposition Author(s): Contreras, G.F., Shen, R., Latorre, R., Perozo, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of voltage-dependent gating in BK channels.

Contreras, G.F., Shen, R., Latorre, R., Perozo, E.

(2025) Nat Commun 16: 5846-5846

PubMed: 40593533 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-60639-y
Primary Citation of Related Structures:
9DI8, 9DIC, 9DIT, 9DJV, 9DKF, 9DKL, 9DKN

PubMed Abstract:
The allosteric communication between the pore domain, voltage sensors, and Ca ²⁺ binding sites in the calcium- and voltage-activated K ⁺ channel (BK) underlies its physiological role as the preeminent signal integrator in excitable systems. BK displays shallow voltage sensitivity with very fast gating charge kinetics, yet little is known about the molecular underpinnings of this distinctive behavior. Here, we explore the mechanistic basis of coupling between voltage-sensing domains (VSDs) and calcium sensors in Aplysia BK by locking the VSDs in their activated (R196Q and R199Q) and resting (R202Q) states, with or without calcium. Cryo-EM structures of these mutants reveal unique tilts at the S4 C-terminal end, together with large side-chain rotameric excursions of the gating charges. Notably, the VSD resting structure (R202Q) also revealed BK in its elusive, fully closed state, highlighting the reciprocal relation between calcium and voltage sensors. These structures provide a plausible path where voltage and Ca ²⁺ binding couple energetically and define the conformation of the pore domain and, thus, BK's full functional range.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Macromolecule Content

Total Structure Weight: 479.31 kDa
Atom Count: 28,220
Modeled Residue Count: 3,596
Deposited Residue Count: 4,260
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BK channel	A, B, C, D	1,065	Aplysia californica	Mutation(s): 2
UniProt
Find proteins for Q5QJC5 (Aplysia californica) Explore Q5QJC5 Go to UniProtKB: Q5QJC5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5QJC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	K [auth A] L [auth A] N [auth B] O [auth B] Q [auth C] K [auth A], L [auth A], N [auth B], O [auth B], Q [auth C], S [auth D], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	J [auth A], M [auth B], P [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D]