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- EMDB-11239: Map of Torpedo nicotinic acetylcholine receptor obtained from hel... -

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Basic information

Entry
Database: EMDB / ID: EMD-11239
TitleMap of Torpedo nicotinic acetylcholine receptor obtained from helical membrane tubes
Map dataAverage map of membrane-bound resting-state Torpedo nicotinic acetylcholine receptor, obtained from 2 helical families ((-16,6) and (-17,5))
Sample
  • Complex: Nicotinic acetylcholine receptor
Function / homology
Function and homology information


acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine receptor signaling pathway / transmembrane signaling receptor activity / postsynaptic membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / 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
Acetylcholine receptor subunit alpha / Acetylcholine receptor delta subunit / Acetylcholine receptor gamma subunit / Acetylcholine receptor beta subunit
Similarity search - Component
Biological speciesTorpedo marmorata (marbled electric ray)
Methodhelical reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsUnwin N
CitationJournal: Iucrj / Year: 2020
Title: Protein-lipid architecture of a cholinergic postsynaptic membrane
Authors: Unwin N
History
DepositionJun 29, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11239.png

Downloads & links

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Map

FileDownload / File: emd_11239.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAverage map of membrane-bound resting-state Torpedo nicotinic acetylcholine receptor, obtained from 2 helical families ((-16,6) and (-17,5))
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. 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: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.017447364 - 0.046507176
Average (Standard dev.)0.00027804924 (±0.0024836066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z268.000268.000268.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0170.0470.000

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Supplemental data

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Sample components

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Entire : Nicotinic acetylcholine receptor

EntireName: Nicotinic acetylcholine receptor
Components
  • Complex: Nicotinic acetylcholine receptor

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Supramolecule #1: Nicotinic acetylcholine receptor

SupramoleculeName: Nicotinic acetylcholine receptor / type: complex / ID: 1 / Parent: 0
Details: Heteropentamric ion channel comprised of two alpha subunits, beta, gamma and delta
Source (natural)Organism: Torpedo marmorata (marbled electric ray) / Organ: electric organ / Tissue: modified muscle tissue / Organelle: postsynaptic membrane / Location in cell: synapse
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 - Concentration: 100.0 mM / Component - Formula: (CH3)2AsO2Na / Component - Name: sodium cacodylate / Details: Solution contains 1mM CaCl2
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 282 K / Instrument: HOMEMADE PLUNGER
Detailsmembrane tubes with acetylcholine receptors arranged on a helical surface lattice

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 100 / Number real images: 2411 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 / Details: 79 frames per micrograph
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.8 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 1.0 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

DetailsThis map is simply an average of two maps of the protein derived from two families of helical membrane tubes. (-16,6) tubes: 1037 images, 51921 segments (-17,5) tubes: 1374 images, 71741 segments
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1 and 3.0)
Details: FSC is based on comparison of aligned particles cut out from the the two individual helical reconstructions
Number images used: 123662
CTF correctionSoftware - Name: Gctf
Details: CTF amplitude correction was applied locally along the axis of each tube, using the non dose-weighted images
Segment selectionNumber selected: 123662
Final angle assignmentType: NOT APPLICABLE

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