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- EMDB-50747: Closed and disordered conformation of the pentameric ligand-gated... -

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Basic information

Entry
Database: EMDB / ID: EMD-50747
TitleClosed and disordered conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10mM EDTA
Map data
Sample
  • Organelle or cellular component: Pentameric ligan-gated ion channel DeCLIC
    • Protein or peptide: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
KeywordsPentameric ligand-gated ion channel / MEMBRANE PROTEIN / pLGIC
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 speciesDesulfacinum sp. (bacteria) / Desulfofustis sp. PB-SRB1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsRovsnik U / Anden O / Lycksell M / Delarue M / Howard RJ / Lindahl E
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structural characterization of pH-modulated closed and open states in a pentameric ligand-gated ion channel
Authors: Rovsnik U / Anden O / Lycksell M / Delarue M / Howard RJ / Lindahl E
History
DepositionJun 24, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50747.png

Downloads & links

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Map

FileDownload / File: emd_50747.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.046750277 - 0.06730529
Average (Standard dev.)0.00041303312 (±0.0025754476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.5952 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50747_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50747_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50747_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric ligan-gated ion channel DeCLIC

EntireName: Pentameric ligan-gated ion channel DeCLIC
Components
  • Organelle or cellular component: Pentameric ligan-gated ion channel DeCLIC
    • Protein or peptide: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein

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Supramolecule #1: Pentameric ligan-gated ion channel DeCLIC

SupramoleculeName: Pentameric ligan-gated ion channel DeCLIC / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Desulfacinum sp. (bacteria)

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Macromolecule #1: Neurotransmitter-gated ion-channel ligand-binding domain-containi...

MacromoleculeName: Neurotransmitter-gated ion-channel ligand-binding 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: 67.891492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TEGRVQHFTG YIEDGRGIFY SLPDMKQGDI IYASMQNTGG NLDPLVGIMA EEIDPAVSLG QVLEKALASE NDLISELTAV ADRIFLGWD DDGGKGYSAS LEFTIPRDGT YHIFAGSTIT NQRLDKFQPT YTTGSFQLIL GLNAPQVISG EGEPEGEVFA S LASLEIKP ...String:
TEGRVQHFTG YIEDGRGIFY SLPDMKQGDI IYASMQNTGG NLDPLVGIMA EEIDPAVSLG QVLEKALASE NDLISELTAV ADRIFLGWD DDGGKGYSAS LEFTIPRDGT YHIFAGSTIT NQRLDKFQPT YTTGSFQLIL GLNAPQVISG EGEPEGEVFA S LASLEIKP EAHVQELEIR LDKDTRYLTQ HTRNLQPGDT FHALVEPIGE APLPRLRLTD SGGKPLAFGL IDQPGESVEL NY TCDQDIC ELVVHVDGTD GQKDSGEAVY RLLVGINAPN LRESGQTPVG SSVFLESDLV TVGLAVDQIV GVDQRSENFS VVG TLKLSW HDPKLGFSPD QCGCTVKSFE DASIRAVAGE INLPLPSFSF YNQQGNRWSQ NQVIFVTPDG RASYFERFTV TLQA PDFDF LAYPFDRQKF SIKVDLAVPT NMFIFNEIER FQQVVGDQLG EEEWVVTSYS QEITEVPFER GSTNSRFTTT LLVKR NLEY YILRIFVPLF LIISVSWVIF FLKDYGRQLE VASGNLLVFV AFNFTISGDL PRLGYLTVLD RFMIVSFCLT AIVVLI SVC QKRLGAVGKQ AVAAQIDTWV LVIYPLVYSL YIIWVYLRFF TDHIGW

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 5 / Component - Concentration: 10.0 mM / Component - Name: EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
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) / Number real images: 26757 / Average exposure time: 2.0 sec. / Average electron dose: 43.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3500000
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 169000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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