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Yorodumi- EMDB-14946: Map2 from paper entitled: Structure of a cholinergic cell membrane -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14946 | |||||||||
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Title | Map2 from paper entitled: Structure of a cholinergic cell membrane | |||||||||
Map data | Density map of acetylcholine receptors in native lipid bilayer obtained by helical reconstruction of tubular vesicles from Torpedo | |||||||||
Sample |
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Keywords | cholesterol / phospholipid / lipid bilayer / acetylcholine receptor / membrane protein | |||||||||
Biological species | Torpedo marmorata (marbled electric ray) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Unwin N | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Structure of a cholinergic cell membrane. Authors: Nigel Unwin / Abstract: Cell membranes are complex assemblies of proteins and lipids making transient or long-term associations that have yet to be characterized at a molecular level. Here, cryo-electron microscopy is ...Cell membranes are complex assemblies of proteins and lipids making transient or long-term associations that have yet to be characterized at a molecular level. Here, cryo-electron microscopy is applied to determine how phospholipids and cholesterol arrange between neighboring proteins (nicotinic acetylcholine receptors) of cholinergic membrane. The lipids exhibit distinct properties in the two leaflets of the bilayer, influenced by the protein surfaces and by differences in cholesterol concentration. In the outer leaflet, the lipids show no consistent motif away from the protein surfaces, in keeping with their assumed fluidity. In the inner leaflet, where the cholesterol concentration is higher, the lipids organize into extensive close-packed linear arrays. These arrays are built from the sterol groups of cholesterol and the initial saturated portions of the phospholipid hydrocarbon chains. Together, they create an ordered ∼7 Å-thick "skin" within the hydrophobic core of the bilayer. The packing of lipids in the arrays appears to bear a close relationship to the linear cholesterol arrays that form crystalline monolayers at the air-water interface. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14946.map.gz | 475.2 MB | EMDB map data format | |
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Header (meta data) | emd-14946-v30.xml emd-14946.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_14946.png | 162.8 KB | ||
Filedesc metadata | emd-14946.cif.gz | 4.9 KB | ||
Others | emd_14946_half_map_1.map.gz emd_14946_half_map_2.map.gz | 925.5 MB 965.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14946 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14946 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14946.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Density map of acetylcholine receptors in native lipid bilayer obtained by helical reconstruction of tubular vesicles from Torpedo | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: First half-map
File | emd_14946_half_map_1.map | ||||||||||||
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Annotation | First half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half-map
File | emd_14946_half_map_2.map | ||||||||||||
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Annotation | Second half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cholinergic cell membrane
Entire | Name: Cholinergic cell membrane |
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Components |
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-Supramolecule #1: Cholinergic cell membrane
Supramolecule | Name: Cholinergic cell membrane / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Tubular vesicles obtained from acetycholine receptor-rich cell membranes, isolated from Torpedo electric organ |
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Source (natural) | Organism: Torpedo marmorata (marbled electric ray) / Organ: electric / Tissue: electric organ tissue / Organelle: electrocyte / Location in cell: synapse |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 / Component - Concentration: 100.0 mM / Component - Formula: C2H6AsNaO2 / Component - Name: sodium cacodylate |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: HOMEMADE PLUNGER Details: blot until filter paper loses water-contact to grid surface (~5 secs).. |
Details | The tubular vesicles are comprised of nicotinic acetylcholine receptors in a cholesterol-rich phospholipid bilayer. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 90.0 K / Max: 90.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 160 / Number real images: 1993 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 Details: Images were collected in movie mode at 40 frames per second |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Segment selection | Number selected: 106333 / Software - Name: RELION (ver. 2.1) Details: Reduced to 91157 segments after 2D classification. 11084 segments used for final density map. |
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Startup model | Type of model: OTHER Details: Low resolution map of tubular vesicle determined originally from layer-line data and Fourier-Bessel synthesis. |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Number classes used: 1 Applied symmetry - Helical parameters - Δz: 5.83 Å Applied symmetry - Helical parameters - Δ&Phi: 146.971 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) Details: The reported FSC was calculated from a 200px volume cut out from the full 800px map. This volume includes the receptor and lipid bilayer, but masks out disordered protein (attributed to ...Details: The reported FSC was calculated from a 200px volume cut out from the full 800px map. This volume includes the receptor and lipid bilayer, but masks out disordered protein (attributed to raspyn) at the base of the receptor Number images used: 11084 |
Details | The selected images were drift-corrected and dose-weighted. |