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    - EMDB-2071: Gating movement in acetylcholine receptor analysed by time-resolv... -

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    Basic information

    Entry
    Database: EMDB / ID: 2071
    TitleGating movement in acetylcholine receptor analysed by time-resolved electron cryo-microscopy
    Keywordsacetylcholine receptor / freeze-trapping / asymmetric gating / allosteric mechanism
    Samplenicotinic acetylcholine receptor in native postsynaptic membrane from Torpedo marmorata
    SourceTorpedo marmorata / fish / marbled electric ray / image: Torpedo californica
    Map dataDensity map of acetylcholine receptor
    Methodhelical reconstruction, at 6.2 A resolution
    AuthorsUnwin N / Fujiyoshi Y
    CitationJ. Mol. Biol., 2012, 422, 617-634

    J. Mol. Biol., 2012, 422, 617-634 StrPapers
    Gating movement of acetylcholine receptor caught by plunge-freezing.
    Nigel Unwin / Yoshinori Fujiyoshi

    DateDeposition: Apr 12, 2012 / Header (metadata) release: Apr 17, 2012 / Map release: Aug 1, 2012 / Last update: Apr 12, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4aq5
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_2071.map.gz (map file in CCP4 format, 10753 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    168 pix
    1 A/pix
    = 168. A
    128 pix
    1 A/pix
    = 128. A
    128 pix
    1 A/pix
    = 128. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1 A
    Density
    Contour Level:1.2 (by author), 1.2 (movie #1):
    Minimum - Maximum-3.90023351 - 4.90560436
    Average (Standard dev.)0E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions128128168
    Origin000
    Limit127127167
    Spacing128128168
    CellA: 128 A / B: 128 A / C: 168 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z111
    M x/y/z128128168
    origin x/y/z0.0000.0000.000
    length x/y/z128.000128.000168.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ128128168
    MAP C/R/S213
    start NC/NR/NS000
    NC/NR/NS128128168
    D min/max/mean-3.9004.906-0.000

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    Supplemental data

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    Sample components

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    Entire nicotinic acetylcholine receptor in native postsynaptic membrane ...

    EntireName: nicotinic acetylcholine receptor in native postsynaptic membrane from Torpedo marmorata
    Number of components: 1 / Oligomeric State: 5 subunits
    MassTheoretical: 300 kDa / Experimental: 300 kDa
    Measured by: molecular weight based on amino acid sequence data and attached sugars

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    Component #1: protein, nicotinic acetylcholine receptor

    ProteinName: nicotinic acetylcholine receptor / a.k.a: nicotinic receptor / Oligomeric Details: pentamer
    Details: Protein is embedded in postsynaptic membrane isolated from Torpedo marmorata electric organ
    Recombinant expression: No
    MassTheoretical: 300 kDa / Experimental: 300 kDa
    SourceSpecies: Torpedo marmorata / fish / marbled electric ray / image: Torpedo californica
    Source (natural)Organelle: plasma membrane / Location in cell: plasma membrane / Cell: electrocyte cells / Organ or tissue: electric organ

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    Experimental details

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    Sample preparation

    Specimen statehelical array
    Helical parametersHand: RIGHT HANDED
    Crystal grow detailsTubular membrane crystals of acetylcholine receptors grow spontaneously from isolated postsynaptic membranes when incubated in low salt buffer at 17 degrees C for two weeks
    Sample solutionBuffer solution: 100 mM sodium cacodylate, 1 mM calcium chloride
    pH: 7
    Support film300 mesh copper grid with pre-irradiated thick holey carbon support, glow discharged in amylamine atmosphere
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 85 %
    Method: Blot until applied droplet loses contact with filter paper (indicated by loss of transparency; typically 6s)
    Time resolved state: Vitrified within 10ms of exposure to acetylcholine (applied as the grid is being plunged,using a fine, focussed spray positioned about 1cm above the ethane surface)
    Details: Vitrification carried out at an ambient temperature of 8 degrees C

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3000SFF / Date: Nov 1, 2005
    Details: Standard low dose imaging of specimens over holes in the carbon support film
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 40000 X (nominal), 38500 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected based on appearance of carbon film at 250,000 times magnification
    Cs: 1.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 2000 nm
    Specimen HolderHolder: Top-entry holder for liquid helium cooled stage (the temperature of the specimen in this holder is usually at 4K)
    Model: OTHER / Temperature: 10 K ( 10 - 20 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 111 / Scanner: OTHER / Sampling size: 2.5 microns / Bit depth: 16 / OD range: 1
    Details: All images recorded on film, developed in Kodak d19 developer

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    Image processing

    ProcessingMethod: helical reconstruction
    Details: Alignment and distortion correction of each tube image was done using a segmental Fourier-Bessel method (Beroukhim & Unwin (1997) Ultramicroscopy, 70:57-81) with 50% overlap between successive segments
    3D reconstructionResolution method: FSC 0.5
    Details: Final maps were calculated from 111 tube images(closed class) and 123 tube images (open class)
    Software: MRC, and, own, programs / Algorithm: Standard Fourier-Bessel synthesis / CTF correction: Each tube image / Resolution: 6.2 A

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    Atomic model buiding

    Modeling #1Software: DireX / Refinement protocol: flexible / Refinement space: REAL
    Details: Protocol: Maximisation of correlation between experimental densities and atomic model, using a deformable elastic network algorithm. Identical refinement procedures were applied to both density maps. The fits were validated by applying the same refinement procedures to independent density maps calculated from half-datasets
    Input PDB model: 2BG9
    Chain ID: A, B, C, D, E
    Output model

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