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- PDB-7pxg: Verruculogen-bound Drosophila Slo channel -

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Basic information

Entry
Database: PDB / ID: 7pxg
TitleVerruculogen-bound Drosophila Slo channel
ComponentsIsoform J of Calcium-activated potassium channel slowpoke
KeywordsTRANSPORT PROTEIN / Potassium transport / BK channel
Function / homology
Function and homology information


Sperm Motility And Taxes / negative regulation of neuromuscular synaptic transmission / male courtship behavior, veined wing generated song production / regulation of synaptic assembly at neuromuscular junction / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / circadian behavior / monoatomic ion channel complex / potassium ion transmembrane transport / potassium ion transport ...Sperm Motility And Taxes / negative regulation of neuromuscular synaptic transmission / male courtship behavior, veined wing generated song production / regulation of synaptic assembly at neuromuscular junction / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / circadian behavior / monoatomic ion channel complex / potassium ion transmembrane transport / potassium ion transport / circadian rhythm / postsynaptic membrane / neuron projection / response to xenobiotic stimulus / neuronal cell body / membrane / plasma membrane
Similarity search - Function
: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / RCK N-terminal domain profile. / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-6PL / Verruculogen / CHOLESTEROL / : / Calcium-activated potassium channel slowpoke
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsRaisch, T. / Brockmann, A. / Ebbinghaus-Kintscher, U. / Freigang, J. / Gutbrod, O. / Kubicek, J. / Maertens, B. / Hofnagel, O. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM.
Authors: Tobias Raisch / Andreas Brockmann / Ulrich Ebbinghaus-Kintscher / Jörg Freigang / Oliver Gutbrod / Jan Kubicek / Barbara Maertens / Oliver Hofnagel / Stefan Raunser /
Abstract: Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca concentrations and are ...Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca 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-bound and Ca-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-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 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.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Isoform J of Calcium-activated potassium channel slowpoke
B: Isoform J of Calcium-activated potassium channel slowpoke
C: Isoform J of Calcium-activated potassium channel slowpoke
D: Isoform J of Calcium-activated potassium channel slowpoke
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,94836
Polymers523,6764
Non-polymers10,27232
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27690 Å2
ΔGint-278 kcal/mol
Surface area148440 Å2
MethodPISA

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isoform J of Calcium-activated potassium channel slowpoke / dSlo / BK channel / Maxi K channel / MaxiK


Mass: 130919.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: slo, CG10693 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03720

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Non-polymers , 6 types, 32 molecules

#2: Chemical
ChemComp-8H5 / Verruculogen


Mass: 511.567 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-6PL / (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 763.100 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#6: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Slo tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4085: / Classification: refinement
EM software
IDNameVersionCategory
1crYOLO1.7particle selection
4CTFFIND4CTF correction
9PHENIX1.19model refinement
10SPHIRE1.3initial Euler assignment
11SPHIRE1.3final Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14SPHIRE1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1131410
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66077 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5TJ6

5tj6


Accession code: 5TJ6 / Source name: PDB / Type: experimental model

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