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- EMDB-13792: Pentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM EDTA -

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Basic information

Entry
Database: EMDB / ID: EMD-13792
TitlePentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM EDTA
Map data
Sample
  • Complex: Pentameric ligand-gated ion channel DeCLIC
    • Protein or peptide: Neur_chan_LBD domain-containing protein
Keywordsion channel / ligand-gated channel / pentameric channel / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLycksell M / Rovsnik U
Funding support Sweden, 3 items
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, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13792.png

Downloads & links

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Map

FileDownload / File: emd_13792.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0139
Minimum - Maximum-0.064640306 - 0.10085898
Average (Standard dev.)0.00034484515 (±0.0037863404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13792_msk_1.map
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Additional map: #1

Fileemd_13792_additional_1.map
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Half map: #1

Fileemd_13792_half_map_1.map
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Half map: #2

Fileemd_13792_half_map_2.map
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Sample components

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Entire : Pentameric ligand-gated ion channel DeCLIC

EntireName: Pentameric ligand-gated ion channel DeCLIC
Components
  • Complex: Pentameric ligand-gated ion channel DeCLIC
    • Protein or peptide: Neur_chan_LBD domain-containing protein

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Supramolecule #1: Pentameric ligand-gated ion channel DeCLIC

SupramoleculeName: Pentameric ligand-gated ion channel DeCLIC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)
Molecular weightTheoretical: 364.31 kDa/nm

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Macromolecule #1: Neur_chan_LBD domain-containing protein

MacromoleculeName: Neur_chan_LBD domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)
Molecular weightTheoretical: 71.733992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHNLQQLLPT RSLIWIFSFL TSISIWCTVA HAETEGRVQH FTGYIEDGRG IFYSLPDMKQ GDIIYASMQN TGGNLDPLVG IMAEEIDPA VSLGQVLEKA LASENDLISE LTAVADRIFL GWDDDGGKGY SASLEFTIPR DGTYHIFAGS TITNQRLDKF Q PTYTTGSF ...String:
MHNLQQLLPT RSLIWIFSFL TSISIWCTVA HAETEGRVQH FTGYIEDGRG IFYSLPDMKQ GDIIYASMQN TGGNLDPLVG IMAEEIDPA VSLGQVLEKA LASENDLISE LTAVADRIFL GWDDDGGKGY SASLEFTIPR DGTYHIFAGS TITNQRLDKF Q PTYTTGSF QLILGLNAPQ VISGEGEPEG EVFASLASLE IKPEAHVQEL EIRLDKDTRY LTQHTRNLQP GDTFHALVEP IG EAPLPRL RLTDSGGKPL AFGLIDQPGE SVELNYTCDQ DICELVVHVD GTDGQKDSGE AVYRLLVGIN APNLRESGQT PVG SSVFLE SDLVTVGLAV DQIVGVDQRS ENFSVVGTLK LSWHDPKLGF SPDQCGCTVK SFEDASIRAV AGEINLPLPS FSFY NQQGN RWSQNQVIFV TPDGRASYFE RFTVTLQAPD FDFLAYPFDR QKFSIKVDLA VPTNMFIFNE IERFQQVVGD QLGEE EWVV TSYSQEITEV PFERGSTNSR FTTTLLVKRN LEYYILRIFV PLFLIISVSW VIFFLKDYGR QLEVASGNLL VFVAFN FTI SGDLPRLGYL TVLDRFMIVS FCLTAIVVLI SVCQKRLGAV GKQAVAAQID TWVLVIYPLV YSLYIIWVYL RFFTDHI GW

UniProtKB: Uncharacterized protein

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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

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v4s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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