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    Yorodumi
    - EMDB-2055: Acetylcholine-binding protein in the hemolymph of the planorbid s... -

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    Basic information

    Entry
    Database: EMDB / ID: 2055
    TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)
    Keywordsligand gated ion channel / LGIC / Cys-loop receptor / AChBP / acetylcholine binding protein / acetylcholine / AChR / acetylcholine receptor / Myasthenia gravis / pentagonal dodecahedron / nicotinic / dodecahedron / Schistosoma mansoni / bilharziosis / Biomphalaria glabrata / snail
    SampleAcetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
    SourceBiomphalaria glabrata / invertebrata
    Map dataA negative temperature factor of 278.9 A^2 was applied to the map.
    Methodsingle particle (icosahedral) reconstruction, at 6 A resolution
    AuthorsSaur M / Moeller V / Kapetanopoulos K / Braukmann S / Gebauer W / Tenzer S / Markl J
    CitationPLoS ONE, 2012, 7, e43685-e43685

    PLoS ONE, 2012, 7, e43685-e43685 StrPapers
    Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits).
    Michael Saur / Vanessa Moeller / Katharina Kapetanopoulos / Sandra Braukmann / Wolfgang Gebauer / Stefan Tenzer / Jürgen Markl

    DateDeposition: Mar 19, 2012 / Header (metadata) release: Apr 5, 2012 / Map release: Aug 29, 2012 / Last update: Mar 19, 2012

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    Structure visualization

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    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1
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    • Surface view with fitted model
    • Atomic models: : PDB-4aod
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4aoe
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_2055.map.gz (map file in CCP4 format, 91383 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    286 pix
    1 A/pix
    = 286. A
    286 pix
    1 A/pix
    = 286. A
    286 pix
    1 A/pix
    = 286. 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 (by author), 1 (movie #1):
    Minimum - Maximum-0.59094787 - 3.62690711
    Average (Standard dev.)0.14051077 (0.43470621)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions286286286
    Origin000
    Limit285285285
    Spacing286286286
    CellA=B=C: 286 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z111
    M x/y/z286286286
    origin x/y/z0.0000.0000.000
    length x/y/z286.000286.000286.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS286286286
    D min/max/mean-0.5913.6270.141

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    Supplemental data

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    Sample components

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    Entire Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata

    EntireName: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
    Number of components: 1
    MassTheoretical: 1.86 MDa / Experimental: 1.86 MDa / Measured by: SDS-PAGE

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    Component #1: protein, Biomphalaria glabrata Acetylcholine Binding Protein

    ProteinName: Biomphalaria glabrata Acetylcholine Binding Protein / a.k.a: BgAChBP / Oligomeric Details: Dodecapentamer
    Details: As yet, it is not entirely clear whether the dodecahedron is a homomeric assembly of either type one and/or two, or a heteromeric assembly of types one and two.
    Recombinant expression: No / Number of Copies: 60
    MassTheoretical: 1.86 MDa / Experimental: 1.86 MDa
    SourceSpecies: Biomphalaria glabrata / invertebrata
    Source (natural)Organ or tissue: Hemolymph

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1.2 mg/ml
    Buffer solution: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl
    pH: 7.4
    Support filmC-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA
    VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 97 K / Humidity: 97 % / Method: 2 x3.5 microlitres with 2 x 3s blotting

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    Electron microscopy imaging #1

    ImagingMicroscope: FEI TECNAI F20 / Date: Jun 4, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal)
    Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 101 K
    CameraDetector: KODAK SO-163 FILM

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    Electron microscopy imaging #2

    ImagingMicroscope: FEI TECNAI F20 / Date: May 25, 2011
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal)
    Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 101 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 151 / Scanner: PRIMESCAN / Sampling size: 5 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction
    Details: manual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references
    Number of projections: 8374 / Number of class averages: 608 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Projection matching / Software: EMAN1.9 / CTF correction: per micrograph / Resolution: 6 A / Resolution method: FSC 0.5

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    Output model

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