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- EMDB-50744: Closed conformation of the pentameric ligand-gated ion channel, D... -

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Basic information

Entry
Database: EMDB / ID: EMD-50744
TitleClosed conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10 mM Ca2+
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
  • Ligand: CALCIUM ION
KeywordsPentameric ligand-gated ion channel / bacterial ion 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 speciesDesulfacinum sp. (bacteria) / Desulfofustis sp. PB-SRB1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50744.png

Downloads & links

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Map

FileDownload / File: emd_50744.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: 2.3
Minimum - Maximum-17.640219999999999 - 27.334585000000001
Average (Standard dev.)-0.000000000002171 (±1.0)
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_50744_msk_1.map
Projections & Slices
AxesZYX

Projections

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
  • Ligand: CALCIUM ION

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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: #1
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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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration3.5 mg/mL
BufferpH: 5 / Component - Concentration: 10.0 mM / Component - Formula: CaCl2 / Component - Name: Calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 26259 / Average exposure time: 2.0 sec. / Average electron dose: 43.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5000000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 22000
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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