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- EMDB-50031: CryoEM structure of sTeLIC nanodisc in closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-50031
TitleCryoEM structure of sTeLIC nanodisc in closed state
Map data
Sample
  • Complex: sTeLIC nanodisc
    • Protein or peptide: Cys-loop ligand-gated ion channel
  • Ligand: DODECANE
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE
  • Ligand: HEXANE
  • Ligand: DECANE
  • Ligand: water
KeywordsIon channel / TRANSLOCASE
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / membrane
Similarity search - Function
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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesendosymbiont of Tevnia jerichonana (vent Tica) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsFan C / Howard RJ / Lindahl E
Funding support1 items
OrganizationGrant numberCountry
Swedish Research Council
CitationJournal: Br J Pharmacol / Year: 2025
Title: Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel.
Authors: Emelia Karlsson / Olivia Andén / Chen Fan / Zaineb Fourati / Ahmed Haouz / Yuxuan Zhuang / Rebecca J Howard / Marc Delarue / Erik Lindahl /
Abstract: BACKGROUND AND PURPOSE: Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) are critical for the action of neurotransmitters and many psychoactive drugs. However, details of their ...BACKGROUND AND PURPOSE: Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) are critical for the action of neurotransmitters and many psychoactive drugs. However, details of their modulatory mechanisms remain unclear, especially beyond the orthosteric neurotransmitter-binding sites. The recently reported prokaryotic symbiont of Tevnia jerichonana ligand-gated ion channel (sTeLIC), a pH-gated homologue of eukaryotic receptors in the pLGIC family, is thought to be modulated by aromatic compounds via a relatively uncharacterised modulatory site in the extracellular vestibule.
EXPERIMENTAL APPROACH: We have characterised the effects of psychostimulant derivatives on sTeLIC using two-electrode voltage-clamp electrophysiology in the presence and absence of engineered ...EXPERIMENTAL APPROACH: We have characterised the effects of psychostimulant derivatives on sTeLIC using two-electrode voltage-clamp electrophysiology in the presence and absence of engineered mutations, and determined X-ray and cryo-EM structures of the channel in both closed and open states.
KEY RESULTS: We have shown that sTeLIC is sensitive to potentiation by several amphiphilic compounds, which preferentially bind to a vestibular pocket in the contracted open-state extracellular domain.
CONCLUSIONS AND IMPLICATIONS: This work provides a detailed structure-function mechanism for allosteric potentiation via a noncanonical ligand site, with potential conservation of the eukaryotic ...CONCLUSIONS AND IMPLICATIONS: This work provides a detailed structure-function mechanism for allosteric potentiation via a noncanonical ligand site, with potential conservation of the eukaryotic pentameric ligand-gated ion channels.
History
DepositionApr 5, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50031.png

Downloads & links

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Map

FileDownload / File: emd_50031.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 420 pix.
= 282.45 Å		0.67 Å/pix.
x 420 pix.
= 282.45 Å		0.67 Å/pix.
x 420 pix.
= 282.45 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.03124631 - 0.04999942
Average (Standard dev.)0.0000061495284 (±0.0010062045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 282.45 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50031_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_50031_half_map_2.map
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Sample components

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Entire : sTeLIC nanodisc

EntireName: sTeLIC nanodisc
Components
  • Complex: sTeLIC nanodisc
    • Protein or peptide: Cys-loop ligand-gated ion channel
  • Ligand: DODECANE
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE
  • Ligand: HEXANE
  • Ligand: DECANE
  • Ligand: water

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Supramolecule #1: sTeLIC nanodisc

SupramoleculeName: sTeLIC nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: endosymbiont of Tevnia jerichonana (vent Tica) (bacteria)

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Macromolecule #1: Cys-loop ligand-gated ion channel

MacromoleculeName: Cys-loop ligand-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: endosymbiont of Tevnia jerichonana (vent Tica) (bacteria)
Molecular weightTheoretical: 37.31082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASLAAEPSD VFIGLKIDQI TGINQKEENF SVVGSLRIDW RQPLLAFEHA PGEPKHRTYT LATFLKLLEE KQIRWPAFTY HNQQGRMDF QNRLISLSED GTVMYLERFT STFQAPAFDF RLFPFDNQLF FIHVDSIFPQ HLFRFQEMQG FSGLGDQLGE E EWIVTEVN ...String:
MASLAAEPSD VFIGLKIDQI TGINQKEENF SVVGSLRIDW RQPLLAFEHA PGEPKHRTYT LATFLKLLEE KQIRWPAFTY HNQQGRMDF QNRLISLSED GTVMYLERFT STFQAPAFDF RLFPFDNQLF FIHVDSIFPQ HLFRFQEMQG FSGLGDQLGE E EWIVTEVN THLTTHNEFT KGDASRFVLE FHAERHLNYY LMRILIPVLL IITVSWFTFF LQDYTKRIDL AGGNLLLFIA FN FTISSDL PRLGYITLMD AFLVGTFIIT ALVVLGNVWL RRLENHGKQA LARKLDIYAI TSYPLAYLLG ALTLWLLFFW RSY

UniProtKB: Cys-loop ligand-gated ion channel

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Macromolecule #2: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 2 / Number of copies: 10 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #3: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 3 / Number of copies: 10 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 5 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #5: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 5 / Number of copies: 5 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 5 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136209
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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