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- EMDB-50194: CryoEM structure of open sTeLIC in detergent, in complex with n-D... -

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Basic information

Entry
Database: EMDB / ID: EMD-50194
TitleCryoEM structure of open sTeLIC in detergent, in complex with n-Dodecyl-Beta-Maltoside
Map data
Sample
  • Organelle or cellular component: Pentameric ligan-gated ion channel sTeLIC
    • Protein or peptide: Cys-loop ligand-gated ion channel
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsPentameric ligand-gated ion channel / cys-loop receptor / pLGIC / MEMBRANE PROTEIN
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: 2.56 Å
AuthorsAnden O / Howard RJ / Lindahl E
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
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 29, 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_50194.png

Downloads & links

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Map

FileDownload / File: emd_50194.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 256 pix.
= 166.4 Å		0.65 Å/pix.
x 256 pix.
= 166.4 Å		0.65 Å/pix.
x 256 pix.
= 166.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.039241686 - 0.0658993
Average (Standard dev.)0.0001413931 (±0.0027325836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 166.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50194_msk_1.map
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Half map: #1

Fileemd_50194_half_map_1.map
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Half map: #2

Fileemd_50194_half_map_2.map
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Sample components

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Entire : Pentameric ligan-gated ion channel sTeLIC

EntireName: Pentameric ligan-gated ion channel sTeLIC
Components
  • Organelle or cellular component: Pentameric ligan-gated ion channel sTeLIC
    • Protein or peptide: Cys-loop ligand-gated ion channel
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Pentameric ligan-gated ion channel sTeLIC

SupramoleculeName: Pentameric ligan-gated ion channel sTeLIC / type: organelle_or_cellular_component / 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: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration7 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 218875
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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