7PXH

Emodepside-bound Drosophila Slo channel

PDB DOI: https://doi.org/10.2210/pdb7PXH/pdb
EM Map EMD-13703: EMDB EMDataResource

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

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: 2.59 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

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27435-w
Primary Citation of 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: 539.2 kDa
Atom Count: 28,922
Modelled Residue Count: 3,540
Deposited Residue Count: 4,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8I2 (Subject of Investigation/LOI) Query on 8I2 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B]	Z [auth B]	(3~{S},6~{R},9~{S},12~{R},15~{S},18~{R},21~{S},24~{R})-4,6,10,16,18,22-hexamethyl-3,9,15,21-tetrakis(2-methylpropyl)-12,24-bis[(4-morpholin-4-ylphenyl)methyl]-1,7,13,19-tetraoxa-4,10,16,22-tetrazacyclotetracosane-2,5,8,11,14,17,20,23-octone C₆₀ H₉₀ N₆ O₁₄ ZMQMTKVVAMWKNY-YSXLEBCMSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
6PL Query on 6PL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] H [auth A] DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], MA [auth D], NA [auth D], OA [auth D], PA [auth D], U [auth B], V [auth B], W [auth B], X [auth B]	(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 DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain L [auth A] SDF format, chain QA [auth D] SDF format, chain Y [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Y [auth B]	HA [auth C], L [auth A], QA [auth D], Y [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain HA [auth C] Focus chain L [auth A] Focus chain QA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth C] Focus chain L [auth A] Focus chain QA [auth D] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	AA [auth C] BA [auth C] E [auth A] F [auth A] JA [auth D] AA [auth C], BA [auth C], E [auth A], F [auth A], JA [auth D], KA [auth D], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	IA [auth C] M [auth A] N [auth A] O [auth A] P [auth A] IA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain IA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain LA [auth D] SDF format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain T [auth B]	CA [auth C], G [auth A], LA [auth D], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain G [auth A] Focus chain LA [auth D] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain G [auth A] Focus chain LA [auth D] Focus chain T [auth B]