7PXG | pdb_00007pxg

Verruculogen-bound Drosophila Slo channel

PDB DOI: https://doi.org/10.2210/pdb7PXG/pdb
EM Map EMD-13702: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Drosophila melanogaster
Expression System: Trichoplusia ni
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2021-10-08 Released: 2021-12-15
Deposition Author(s): Raisch, T., Brockmann, A., Ebbinghaus-Kintscher, U., Freigang, J., Gutbrod, O., Kubicek, J., Maertens, B., Hofnagel, O., Raunser, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM.

Raisch, T., Brockmann, A., Ebbinghaus-Kintscher, U., Freigang, J., Gutbrod, O., Kubicek, J., Maertens, B., Hofnagel, O., Raunser, S.

(2021) Nat Commun 12: 7164-7164

PubMed: 34887422 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27435-w
Primary Citation Related Structures:
7PXE, 7PXF, 7PXG, 7PXH

PubMed Abstract:
Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca ²⁺ concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca ²⁺-bound and Ca ²⁺-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K ⁺ transport by blocking the Ca ²⁺-induced activation signal and precludes K ⁺ from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K ⁺ coordination and uncouples ion gating from Ca ²⁺ and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels.

Organizational Affiliation

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 533.95 kDa
Atom Count: 28,664
Modeled Residue Count: 3,540
Deposited Residue Count: 4,720
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform J of Calcium-activated potassium channel slowpoke	A, B, C, D	1,180	Drosophila melanogaster	Mutation(s): 0 Gene Names: slo, CG10693 Membrane Entity: Yes
UniProt
Find proteins for Q03720 (Drosophila melanogaster) Explore Q03720 Go to UniProtKB: Q03720
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6PL Query on 6PL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain S [auth B] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain S [auth B] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain S [auth B] mmCIF format, chain BA [auth C]	AA [auth C] BA [auth C] HA [auth D] I [auth A] IA [auth D] AA [auth C], BA [auth C], HA [auth D], I [auth A], IA [auth D], S [auth B], T [auth B], V [auth C]	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE C₄₂ H₈₅ N O₈ P PZNPLUBHRSSFHT-RRHRGVEJSA-O		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C]
8H5 (Subject of Investigation/LOI) Query on 8H5 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	DA [auth D], E [auth A], O [auth B], W [auth C]	Verruculogen C₂₇ H₃₃ N₃ O₇ LRXYHMMJJCTUMY-GWXUGYLUSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth B] SDF format, chain JA [auth D] SDF format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain CA [auth C]	CA [auth C], J [auth A], JA [auth D], U [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain CA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain U [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A]	EA [auth D] F [auth A] FA [auth D] G [auth A] P [auth B] EA [auth D], F [auth A], FA [auth D], G [auth A], P [auth B], Q [auth B], X [auth C], Y [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A], N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] SDF format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain GA [auth D]	GA [auth D], H [auth A], R [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain H [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain H [auth A] Focus chain R [auth B] Focus chain Z [auth C]