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- PDB-7q3g: Pentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM Ca2+ -

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Basic information

Entry
Database: PDB / ID: 7q3g
TitlePentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM Ca2+
ComponentsNeur_chan_LBD domain-containing protein
KeywordsMEMBRANE PROTEIN / ion channel / ligand-gated channel / pentameric channel
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / membrane / metal ion binding
Similarity search - Function
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
Uncharacterized protein
Similarity search - Component
Biological speciesDesulfofustis sp. PB-SRB1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLicksell, M. / Rovsnik, U. / Hanke, A. / Howard, R.J. / Lindahl, E.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
The Swedish Foundation for Strategic Research Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.
Authors: Marie Lycksell / Urška Rovšnik / Anton Hanke / Anne Martel / Rebecca J Howard / Erik Lindahl /
Abstract: Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs, there is architectural diversity ...Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs, there is architectural diversity involving N-terminal domains (NTDs) not found in eukaryotic relatives, exemplified by the calcium-sensitive channel (DeCLIC) from a deltaproteobacterium, which has an NTD in addition to the canonical pLGIC structure. Here, we have characterized the structure and dynamics of DeCLIC through cryoelectron microscopy (cryo-EM), small-angle neutron scattering (SANS), and molecular dynamics (MD) simulations. In the presence and absence of calcium, cryo-EM yielded structures with alternative conformations of the calcium-binding site. SANS profiles further revealed conformational diversity at room temperature beyond that observed in static structures, shown through MD to be largely attributable to rigid-body motions of the NTD relative to the protein core, with expanded and asymmetric conformations improving the fit of the SANS data. This work reveals the range of motion available to the DeCLIC NTD and calcium-binding site, expanding the conformational landscape of the pLGIC family. Further, these findings demonstrate the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate interfacial interactions that are highly conserved in the pLGIC family.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neur_chan_LBD domain-containing protein
E: Neur_chan_LBD domain-containing protein
D: Neur_chan_LBD domain-containing protein
C: Neur_chan_LBD domain-containing protein
B: Neur_chan_LBD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,87010
Polymers358,6705
Non-polymers2005
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28180 Å2
ΔGint-208 kcal/mol
Surface area124130 Å2

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Components

#1: Protein
Neur_chan_LBD domain-containing protein / Ligand-gated ion channel DeCLIC


Mass: 71733.992 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfofustis sp. PB-SRB1 (bacteria) / Gene: N839_03575 / Production host: Escherichia coli (E. coli) / References: UniProt: V4JF97
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / 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: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentameric ligand-gated ion channel DeCLIC / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 364.31 kDa/nm / Experimental value: NO
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19731 / Symmetry type: POINT

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