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- EMDB-53951: SsCl at pH 6.5 + IVM - Partially opened -

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Basic information

Entry
Database: EMDB / ID: EMD-53951
TitleSsCl at pH 6.5 + IVM - Partially opened
Map dataSharp
Sample
  • Organelle or cellular component: Sarcoptes scabies chloride channel (SsCl)
    • Protein or peptide: pH gated chloride channel
  • Ligand: (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
KeywordsIon channel / pLGIC / pH-sensitive channel / Ivermectin / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKleiz-Ferreira J / Brams M / Harrison PJ / Nys M / Gallagher C / Donze Y / Quigley A / Bertrand D / Ulens C
Funding support Belgium, 2 items
OrganizationGrant numberCountry
KU LeuvenC14/23/128 Belgium
Research Foundation - Flanders (FWO)G087921N Belgium
CitationJournal: To Be Published
Title: SsCl at pH 6.5 + IVM - Partially opened
Authors: Kleiz-Ferreira J / Brams M / Harrison PJ / Nys M / Gallagher C / Donze Y / Quigley A / Bertrand D / Ulens C
History
DepositionJun 6, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53951.png

Downloads & links

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Map

FileDownload / File: emd_53951.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 238.752 Å		0.83 Å/pix.
x 288 pix.
= 238.752 Å		0.83 Å/pix.
x 288 pix.
= 238.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.468
Minimum - Maximum-2.4717655 - 3.407157
Average (Standard dev.)0.005429244 (±0.11010854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 238.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53951_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened

Fileemd_53951_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_53951_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_53951_half_map_2.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sarcoptes scabies chloride channel (SsCl)

EntireName: Sarcoptes scabies chloride channel (SsCl)
Components
  • Organelle or cellular component: Sarcoptes scabies chloride channel (SsCl)
    • Protein or peptide: pH gated chloride channel
  • Ligand: (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

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Supramolecule #1: Sarcoptes scabies chloride channel (SsCl)

SupramoleculeName: Sarcoptes scabies chloride channel (SsCl) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarcoptes scabiei (arthropod)

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Macromolecule #1: pH gated chloride channel

MacromoleculeName: pH gated chloride channel / type: protein_or_peptide / ID: 1 / Details: Truncated intracellular region, with a linker. / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sarcoptes scabiei (arthropod)
Molecular weightTheoretical: 39.763938 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NNVIIDETFI KTFNKTDRLI RPSFNDKADV IDVSMLIDRF AYYHDIESIL EIQAQFEYHW FDQRVKFDCD RSSRIEGNHY HEQIWVPDL RVSRTEDIDV FESENLTRLI SIQIDCDGHV RMRFRSNLDL ICVMNYQNYP FDEQTCEIEL IPSYMEINRL Q LRWKDQNI ...String:
NNVIIDETFI KTFNKTDRLI RPSFNDKADV IDVSMLIDRF AYYHDIESIL EIQAQFEYHW FDQRVKFDCD RSSRIEGNHY HEQIWVPDL RVSRTEDIDV FESENLTRLI SIQIDCDGHV RMRFRSNLDL ICVMNYQNYP FDEQTCEIEL IPSYMEINRL Q LRWKDQNI MIRDDFYMSG HLLKGYSVHQ KDVELMPYNE IYSALFVHLH LKRQFIYHIL VLFLPSIFIV LTSWISFWIE IT CIPARVT LCVTTLLAMV TVSKESKQNI PKVPYVKAVD LWFAGCIVSI FITLIEYIFV CYVYRESQPA RAASIDRKCR YLI PLAFIL FNLIHWS

UniProtKB: pH gated chloride channel

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Macromolecule #2: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)...

MacromoleculeName: (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- ...Name: (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
type: ligand / ID: 2 / Number of copies: 5 / Formula: IVM
Molecular weightTheoretical: 875.093 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5506940
CTF correctionSoftware - Name: CTFFIND / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 344703
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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