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- PDB-8f33: ELIC with Propylamine in saposin nanodiscs with 2:1:1 POPC:POPE:POPG -

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Basic information

Entry
Database: PDB / ID: 8f33
TitleELIC with Propylamine in saposin nanodiscs with 2:1:1 POPC:POPE:POPG
ComponentsErwinia chrysanthemi ligand-gated ion channel
KeywordsTRANSPORT PROTEIN / ELIC / ion channel / pLGIC / Structural Protein / Membrane 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: 3.28 Å
AuthorsDalal, V. / Arcario, M.J. / Petroff II, J.T. / Deitzen, N.M. / Tan, B.K. / Brannigan, G. / Cheng, W.W.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137957 United States
CitationJournal: Nat Commun / Year: 2024
Title: Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel.
Authors: Vikram Dalal / Mark J Arcario / John T Petroff / Brandon K Tan / Noah M Dietzen / Michael J Rau / James A J Fitzpatrick / Grace Brannigan / Wayland W L Cheng /
Abstract: Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ...Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)184,69110
Polymers184,3955
Non-polymers2965
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Erwinia chrysanthemi ligand-gated ion channel


Mass: 36879.000 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
Has ligand of interestY

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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: ELIC with Propylamine in saposin nanodiscs 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: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: O2 27.5 sccm H2 6.4 sccm / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Calibrated magnification: 96000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.28 sec. / Electron dose: 47.55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsSpherical aberration corrector: Microscope was equipped with a Cs corrector
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: EPU / Version: 2.12.1.2782 / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84696 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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