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- PDB-9rgp: SsCl at pH 9 + IVM - Opened -

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Basic information

Entry
Database: PDB / ID: 9rgp
TitleSsCl at pH 9 + IVM - Opened
ComponentspH gated chloride channel
KeywordsMEMBRANE PROTEIN / Ion channel / pLGIC / pH-sensitive channel / Ivermectin
Function / homology
Function and homology information


ligand-gated monoatomic anion channel activity / chloride channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / plasma membrane
Similarity search - Function
Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Chem-IVM / pH gated chloride channel
Similarity search - Component
Biological speciesSarcoptes scabiei (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsKleiz-Ferreira, J. / Brams, M. / Harrison, P.J. / Nys, M. / Gallagher, C. / Donze, Y. / Quigley, A. / Bertrand, D. / Ulens, C.
Funding support Belgium, 2items
OrganizationGrant numberCountry
KU LeuvenC14/23/128 Belgium
Research Foundation - Flanders (FWO)G087921N Belgium
CitationJournal: To Be Published
Title: SsCl at pH 9 + IVM - Opened
Authors: Kleiz-Ferreira, J. / Brams, M. / Harrison, P.J. / Nys, M. / Gallagher, C. / Donze, Y. / Quigley, A. / Bertrand, D. / Ulens, C.
History
DepositionJun 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pH gated chloride channel
B: pH gated chloride channel
C: pH gated chloride channel
D: pH gated chloride channel
E: pH gated chloride channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,23111
Polymers177,8205
Non-polymers4,4116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
pH gated chloride channel


Mass: 35564.023 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sarcoptes scabiei (arthropod) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8SDP7
#2: Chemical
ChemComp-IVM / (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside / 22,23-DIHYDROAVERMECTIN B1A / IVERMECTIN


Mass: 875.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C48H74O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiparasitic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Sarcoptes scabies chloride channel (SsCl) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Sarcoptes scabiei (arthropod)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Buffer solutionpH: 9
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
4CTFFINDCTF correction
10RELION5initial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10143236
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87619 / Symmetry type: POINT

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