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    - PDB-4aq9: Gating movement in acetylcholine receptor analysed by time- resol... -

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    Basic information

    Entry
    Database: PDB / ID: 4aq9
    TitleGating movement in acetylcholine receptor analysed by time- resolved electron cryo-microscopy (open class)
    DescriptorACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
    ACETYLCHOLINE RECEPTOR BETA SUBUNIT
    ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
    ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
    KeywordsMEMBRANE PROTEIN / FREEZE-TRAPPING / ASYMMETRIC GATING / ALLOSTERIC MECHANISM
    Specimen sourceTorpedo marmorata / fish / MARBLED ELECTRIC RAY / TORPEDO ELECTRIC RAY / image: Torpedo californica
    MethodElectron microscopy (6.2 A resolution / Helical / Vitreous ice)
    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 13, 2012 / Release: Aug 1, 2012 / Last modification: Sep 25, 2013

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    Assembly

    Deposited unit
    A: ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
    B: ACETYLCHOLINE RECEPTOR BETA SUBUNIT
    C: ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
    D: ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
    E: ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT

    278 kDa, 5 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    278,0705
    Polyers278,0705
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA / PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN / Source: TORPEDO MARMORATA (gene. exp.) / References: UniProt: P02711
    #2polypeptide(L) / ACETYLCHOLINE RECEPTOR BETA SUBUNIT / PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN / Source: TORPEDO MARMORATA (gene. exp.) / References: UniProt: Q6S3I0
    #3polypeptide(L) / ACETYLCHOLINE RECEPTOR DELTA SUBUNIT / PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN / Source: TORPEDO MARMORATA (gene. exp.) / References: UniProt: Q6S3H8
    #4polypeptide(L) / ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT / PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN / Source: TORPEDO MARMORATA (gene. exp.) / References: UniProt: Q6S3H9

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE

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    Sample preparation

    Assembly of specimenName: NICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
    Aggregation state: FILAMENT
    Details: PRELIMINARY SELECTION BY OPTICAL DIFFRACTION THEN EVALUATION OF FOURIER TRANSFORMS
    Buffer solutionName: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE
    Sample preparationpH: 7
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85 TEMPERATURE- 120 INSTRUMENT- HOMEMADE PLUNGER METHOD- BLOT UNTIL APPLIED DROPLET LOSES CONTACT WITH FILTER PAPER (INDICATED BY LOSS OF TRANSPARENCY TYPICALLY 6S) TIMERESOLVEDSTATE- 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

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    Electron microscopy imaging

    MicroscopyMicroscope model: JEOL 3000FS / 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
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 38500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm
    Specimen holderTemperature: 4 K
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 123
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: MRC AND OWN PROGRAMS
    3D reconstructionMethod: STANDARD FOURIER-BESSEL SYNTHESIS / Resolution: 6.2 A / Nominal pixel size: 1 A/pix / Actual pixel size: 1 A/pix / Magnification calibration: CALIBRATION GRID IN MICROSCOPE / CTF correction method: EACH TUBE IMAGE
    Details: FOURIER-BESSEL SYNTHESIS AFTER APPLYING DISTORTION CORRECTIONS TO THE IMAGES SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2072.
    Atomic model buildingMethod: MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX)
    Ref protocol: LOW RESOLUTION X-RAY / Ref space: REAL
    Least-squares processHighest resolution: 6.2 A
    Refine hist #LASTHighest resolution: 6.2 A
    Number of atoms included #LASTProtein: 14924 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 14924

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