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- PDB-9ngc: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:... -

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Basic information

Entry
Database: PDB / ID: 9ngc
TitleELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
ComponentsErwinia chrysanthemi ligand-gated ion channel
KeywordsMEMBRANE PROTEIN / ELIC / ion channel / pLGIC / Structural Protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein 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
3-AMINOPROPANE / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDalal, V. / Cheng, W.W.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137957 United States
American Heart Association24POST1189869 United States
CitationJournal: Elife / Year: 2025
Title: Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes
Authors: Dalal, V. / Tan, B.K. / Xu, H. / Cheng, W.W.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erwinia chrysanthemi ligand-gated ion channel
B: Erwinia chrysanthemi ligand-gated ion channel
C: Erwinia chrysanthemi ligand-gated ion channel
D: Erwinia chrysanthemi ligand-gated ion channel
E: Erwinia chrysanthemi ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,39712
Polymers185,0555
Non-polymers3427
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
Erwinia chrysanthemi ligand-gated ion channel


Mass: 37011.055 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Dickeya dadantii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 56.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsSpherical aberration corrector: Cs Corrected System

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Processing

EM softwareName: EPU / Version: 3.8 / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 422344
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120578 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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