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EMDB-1434: Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecula... - Yorodumi

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    - EMDB-1434: Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecula... -

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    Basic information

    Entry
    Database: EMDB / ID: 1434
    TitleNautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
    SampleNautilus pompilius hemocyanin
    SourceNautilus pompilius / invertebrata
    Map dataThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
    Methodsingle particle reconstruction, at 9.1 A resolution
    AuthorsGatsogiannis C / Moeller A / Depoix F / Meissner U / Markl J
    CitationJ. Mol. Biol., 2007, 374, 465-486

    J. Mol. Biol., 2007, 374, 465-486 StrPapers
    Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
    Christos Gatsogiannis / Arne Moeller / Frank Depoix / Ulrich Meissner / Jürgen Markl

    DateDeposition: Sep 26, 2007 / Header (metadata) release: Sep 26, 2007 / Map release: Sep 30, 2011 / Last update: Sep 26, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0055
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.0055
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1434.map.gz (map file in CCP4 format, 65537 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    256 pix
    1.85 A/pix
    = 473.6 A
    256 pix
    1.85 A/pix
    = 473.6 A
    256 pix
    1.85 A/pix
    = 473.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.85 A
    Density
    Contour Level:0.0055 (by emdb), 0.0055 (movie #1):
    Minimum - Maximum-0.0368309 - 0.0538236
    Average (Standard dev.)0.000232174 (0.00402936)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions256256256
    Origin000
    Limit255255255
    Spacing256256256
    CellA=B=C: 473.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.851.851.85
    M x/y/z256256256
    origin x/y/z0.0000.0000.000
    length x/y/z473.600473.600473.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ10110173
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS256256256
    D min/max/mean-0.0370.0540.000

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    Supplemental data

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    Sample components

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    Entire Nautilus pompilius hemocyanin

    EntireName: Nautilus pompilius hemocyanin
    Oligomeric State: Nautilus pompilius hemocyanin is a decamer of a 350 kDa subunit. Each subunit is composed by 7 paralogous O2 binding functional units.
    Number of components: 1
    MassTheoretical: 3.5 MDa

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    Component #1: protein, Nautilus pompilius hemocyanin

    ProteinName: Nautilus pompilius hemocyanin / a.k.a: Nautilus pompilius hemocyanin / Recombinant expression: No
    MassExperimental: 3.5 MDa
    SourceSpecies: Nautilus pompilius / invertebrata
    Source (natural)Organ or tissue: hemolymph

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.4 mg/ml
    Buffer solution: 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, 150mM NaCl
    pH: 7.4
    Support film400 mesh copper
    Stainingcryo-EM, no stain
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 86 K / Method: Single side blotting and rapid plunging
    Details: Vitrification instrument: home made. Vitrification carried out in 100 percent nitrogen atmosphere

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
    LensMagnification: 49000 X (nominal), 49000 X (calibrated) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3300 nm
    Specimen HolderHolder: Gatan single-tilt cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 86 K
    CameraDetector: KODAK SO-163 FILM

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 5200 / Number of projections: 16000
    Details: The particles were selected using the automatic selection program boxer
    Applied symmetry: C5 (5 fold cyclic)
    3D reconstructionAlgorithm: Common Lines, projection matching / Software: IMAGIC-5 / CTF correction: CTFFIND3 and TRANSFER, IMAGIC 5 / Resolution: 9.1 A / Resolution method: FSC 0.5

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