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- PDB-9rgm: SsCl at pH 6.5 - closed -

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Basic information

Entry
Database: PDB / ID: 9rgm
TitleSsCl at pH 6.5 - closed
ComponentspH gated chloride channel
KeywordsMEMBRANE PROTEIN / Ion channel / pLGIC / pH-sensitive channel
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
pH gated chloride channel
Similarity search - Component
Biological speciesSarcoptes scabiei (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsKleiz-Ferreira, J. / Brams, M. / Harrison, P.J. / Gallagher, C. / Nys, M. / 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: Nat Commun / Year: 2026
Title: Structure of a pH-sensitive pentameric ligand-gated ion channel from the Sarcoptes scabies mite.
Authors: Jessica Kleiz-Ferreira / Marijke Brams / Peter J Harrison / Casey I Gallagher / Mieke Nys / Ysaline Donze / Andrew Quigley / Daniel Bertrand / Chris Ulens /
Abstract: Scabies is a skin infestation caused by the mite Sarcoptes scabiei and represents a substantial global health burden exacerbated by emerging resistance to ivermectin. An anionic pentameric ligand- ...Scabies is a skin infestation caused by the mite Sarcoptes scabiei and represents a substantial global health burden exacerbated by emerging resistance to ivermectin. An anionic pentameric ligand-gated ion channel from the mite, SsCl, shows pH-sensitivity and is significantly modulated by ivermectin. Here, we use cryo-EM and electrophysiology to explore the pH-sensing mechanisms of SsCl and the impact of ivermectin on channel activity. Structures of SsCl were resolved in closed (pH 6.5) and desensitized (pH 9) states, alongside ivermectin-bound conformations. The desensitized structure adopts an unexpected hourglass conformation, suggesting a gating mechanism closer related to cation-selective channels. Structural analysis and mutagenesis identify extracellular histidine and glutamic acid residues that impact the pH-sensitivity, likely contributing to a broader pH-sensing network. Ivermectin-bound structures reveal pH-dependent modulation, enhancing open-state prevalence at pH 9 and enabling atypical activation at pH 6.5. These findings offer initial insights into SsCl's pH-sensitivity and ivermectin's activity, informing next-generation antiparasitic design.
History
DepositionJun 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: 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


Theoretical massNumber of molelcules
Total (without water)200,2015
Polymers200,2015
Non-polymers00
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: 40040.266 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Truncated intracellular region and linker added. / Source: (gene. exp.) Sarcoptes scabiei (arthropod) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8SDP7
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: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Sarcoptes scabiei (arthropod)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Buffer solutionpH: 6.5
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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 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: 892545
3D reconstructionResolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16607 / Symmetry type: POINT
RefinementResolution: 4.24→4.24 Å / Cor.coef. Fo:Fc: 0.967
RfactorNum. reflection% reflection
Rwork0.25452 --
obs0.25452 40666 100 %
Displacement parametersBiso mean: 195.86 Å2
LS refinement shellHighest resolution: 4.24 Å /
Rfactor% reflection
Rfree0 -
Rwork0.853 -
obs-100 %

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