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- EMDB-53950: SsCl at pH 6.5 - closed -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53950
TitleSsCl at pH 6.5 - closed
Map dataSharp
Sample
  • Organelle or cellular component: Sarcoptes scabies chloride channel (SsCl)
    • Protein or peptide: pH gated chloride channel
KeywordsIon channel / pLGIC / pH-sensitive channel / 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: 4.24 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 - closed
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_53950.png

Downloads & links

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Map

FileDownload / File: emd_53950.map.gz / Format: CCP4 / Size: 64 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.)
0.73 Å/pix.
x 256 pix.
= 187.2 Å		0.73 Å/pix.
x 256 pix.
= 187.2 Å		0.73 Å/pix.
x 256 pix.
= 187.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.38235357 - 0.6920757
Average (Standard dev.)0.013280759 (±0.04300782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 187.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53950_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened

Fileemd_53950_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HalfB

Fileemd_53950_half_map_1.map
AnnotationHalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HalfA

Fileemd_53950_half_map_2.map
AnnotationHalfA
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

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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: all
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 and linker added. / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sarcoptes scabiei (arthropod)
Molecular weightTheoretical: 40.040266 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 FNLIHWSYL

UniProtKB: pH gated chloride channel

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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

MicroscopeJEOL CRYO ARM 300
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: 1.9000000000000001 µm / Nominal defocus min: 1.1 µm

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Image processing

Particle selectionNumber selected: 892545
CTF correctionSoftware - Name: CTFFIND / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16607
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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