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- EMDB-14942: Map1 from paper entitled: Structure of a cholinergic cell membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-14942
TitleMap1 from paper entitled: Structure of a cholinergic cell membrane
Map dataDensity map of acetylcholine receptors in native lipid bilayer obtained by helical reconstruction of tubular vesicles from Torpedo
Sample
  • Organelle or cellular component: Cholinergic cell membrane
Keywordscholesterol / phospholipid / lipid bilayer / acetylcholine receptor / membrane protein
Biological speciesTorpedo marmorata (marbled electric ray)
Methodhelical reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsUnwin N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105184294 United Kingdom
CitationJournal: 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
DepositionMay 7, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14942.png

Downloads & links

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Map

FileDownload / File: emd_14942.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of acetylcholine receptors in native lipid bilayer obtained by helical reconstruction of tubular vesicles from Torpedo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0036
Minimum - Maximum-0.012277572 - 0.024115598
Average (Standard dev.)0.0007612494 (±0.003680287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1072.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Second half map

Fileemd_14942_half_map_1.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half-map

Fileemd_14942_half_map_2.map
AnnotationFirst half-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 : Cholinergic cell membrane

EntireName: Cholinergic cell membrane
Components
  • Organelle or cellular component: Cholinergic cell membrane

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Supramolecule #1: Cholinergic cell membrane

SupramoleculeName: Cholinergic cell membrane / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Tubular vesicles obtained from acetycholine receptor-rich cell membranes, isolated from Torpedo electric organ
Source (natural)Organism: Torpedo marmorata (marbled electric ray) / Organ: electric / Tissue: electric organ tissue / Organelle: electrocyte / Location in cell: synapse

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7 / Component - Concentration: 100.0 mM / Component - Formula: C2H6AsNaO2 / Component - Name: sodium cacodylate
GridModel: 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
VitrificationCryogen 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)..
DetailsThe tubular vesicles are comprised of nicotinic acetylcholine receptors in a cholesterol-rich phospholipid bilayer.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 90.0 K
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were drift-corrected and dose-weighted.
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 5.88 Å
Applied symmetry - Helical parameters - Δ&Phi: 146.981 °
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: 11858
Segment selectionNumber selected: 106333 / Software - Name: RELION (ver. 2.1)
Details: Reduced to 91157 segments after 2D classification. 11858 segments used for final density map.
Startup modelType of model: OTHER
Details: Low resolution map of tubular vesicle determined originally from layer-line data and Fourier-Bessel synthesis.
Final angle assignmentType: NOT APPLICABLE

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