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- EMDB-18865: Influence of lipid bilayer on structure of acetylcholine receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-18865
TitleInfluence of lipid bilayer on structure of acetylcholine receptor
Map dataAcetylcholine receptors in tubular vesicle; (-17,5) helical family
Sample
  • Organelle or cellular component: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
KeywordsIon channel / MEMBRANE PROTEIN
Biological speciesTorpedo marmorata (marbled electric ray)
Methodhelical reconstruction / cryo EM / Resolution: 8.5 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: 2024
Title: Influence of lipid bilayer on the structure of the muscle-type nicotinic acetylcholine receptor.
Authors: Nigel Unwin /
Abstract: The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic ...The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic junctions, where it effects rapid depolarization of the postsynaptic membrane in response to acetylcholine released into the synaptic cleft. Previously, cryo-EM of intact membrane from revealed that the lipid bilayer surrounding the junctional receptor has a uniquely asymmetric and ordered structure, due to a high concentration of cholesterol. It is now shown that this special lipid environment influences the transmembrane (TM) folding of the protein. All five submembrane MX helices of the membrane-intact junctional receptor align parallel to the surface of the cholesterol-ordered lipids in the inner leaflet of the bilayer; also, the TM helices in the outer leaflet are splayed apart. However in the structure obtained from the same protein after extraction and incorporation in nanodiscs, the MX helices do not align to a planar surface, and the TM helices arrange compactly in the outer leaflet. Realignment of the MX helices of the nanodisc-solved structure to a planar surface converts their adjoining TM helices into an obligatory splayed configuration, characteristic of the junctional receptor. Thus, the form of the receptor sustained by the special lipid environment of the synaptic junction is the one that mediates fast synaptic transmission; whereas, the nanodisc-embedded protein may be like the extrajunctional form, existing in a disordered lipid environment.
History
DepositionNov 9, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18865.png

Downloads & links

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Map

FileDownload / File: emd_18865.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcetylcholine receptors in tubular vesicle; (-17,5) helical family
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: 0.005
Minimum - Maximum-0.012430608 - 0.02487273
Average (Standard dev.)0.0008828348 (±0.0038352846)
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: Acetylcholine receptors in tubular vesicle; (-17,5) helical family

Fileemd_18865_half_map_1.map
AnnotationAcetylcholine receptors in tubular vesicle; (-17,5) helical family
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Acetylcholine receptors in tubular vesicle; (-17,5) helical family

Fileemd_18865_half_map_2.map
AnnotationAcetylcholine receptors in tubular vesicle; (-17,5) helical family
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Muscle-type nicotinic acetylcholine receptor in intact synaptic m...

EntireName: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
Components
  • Organelle or cellular component: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane

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Supramolecule #1: Muscle-type nicotinic acetylcholine receptor in intact synaptic m...

SupramoleculeName: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Postsynaptic membranes were isolated from fresh electric organ and incubated in low salt buffer to form ordered arrays of acetylcholine receptors in tubular vesicles
Source (natural)Organism: Torpedo marmorata (marbled electric ray)
Molecular weightTheoretical: 290 KDa

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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:
ConcentrationFormulaName
100.0 mMC2H7AsO2sodium cacodylate
1.0 mMCaCl2calcium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: HOMEMADE PLUNGER
DetailsSpecimen comprises tubular vesicles which are imaged in thin ice over holes in the support film

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: 1.2 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsAll images taken manually: by searching at low magnification for long straight and narrow tubes, then recording in integrating mode
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 200 / Number real images: 4045 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Details: Images were collected in integrating mode, 2 seconds exposure
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 160652 / Software - Name: RELION (ver. 2.1 and 3.1)
Details: 160652 tube segments from 4045 selected micrographs were reduced to 107524 tube segments after 2D classification
Startup modelType of model: OTHER
Details: Original model was a map of the tube obtained by Fourier-Bessel reconstruction
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 5.88 Å
Applied symmetry - Helical parameters - Δ&Phi: 146.976 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 5206
DetailsImages of appropriate helical families were selected on the basis of their FFTs, then drift-corrected and dose-weighted

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7smm

chain_id: A, residue_range: 212-433, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm
chain_id: B, residue_range: 226-479
chain_id: C, residue_range: 218-460
chain_id: D, residue_range: 212-433
chain_id: E, residue_range: 220-472
DetailsRefinement parameters were chosen to minimise changes to the original secondary structure
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 350

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