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    Yorodumi
    - EMDB-1059: Electron cryomicroscopy structure of N-ethyl maleimide sensitive ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1059
    TitleElectron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
    SampleNSF alpha-SNAP SNARE 20S
    SourceCricetulus griseus / mammal / Chinese Hamster
    Bos taurus / mammal / Cattle /
    Unidentified / Chinese Hamster
    Map data3D density map of NSF?alpha-SNAP?SNARE (20S)
    Methodsingle particle reconstruction, at 11 A resolution
    AuthorsFurst J / Sutton RB / Chen J / Brunger AT / Grigorieff N
    CitationEMBO J., 2003, 22, 4365-4374

    EMBO J., 2003, 22, 4365-4374 StrPapers
    Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
    Johannes Furst / R Bryan Sutton / James Chen / Axel T Brunger / Nikolaus Grigorieff

    DateDeposition: Oct 10, 2003 / Header (metadata) release: Oct 10, 2003 / Map release: Oct 10, 2003 / Last update: Oct 10, 2003

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.736926654
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 0.736926654
    • Imaged by UCSF CHIMERA
    • Download
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    Map

    Fileemd_1059.map.gz (map file in CCP4 format, 2849 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    90 pix
    3.5 A/pix
    = 315. A
    90 pix
    3.5 A/pix
    = 315. A
    90 pix
    3.5 A/pix
    = 315. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.5 A
    Density
    Contour Level:0.144, 0.7369267 (movie #1):
    Minimum - Maximum-0.681735 - 1.45625
    Average (Standard dev.)0.0257073 (0.145834)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions909090
    Origin111
    Limit909090
    Spacing909090
    CellA=B=C: 315 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.53.53.5
    M x/y/z909090
    origin x/y/z0.0000.0000.000
    length x/y/z315.000315.000315.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ0052
    NX/NY/NZ12812855
    MAP C/R/S123
    start NC/NR/NS111
    NC/NR/NS909090
    D min/max/mean-0.6821.4560.026

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    Supplemental data

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    Sample components

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    Entire NSF alpha-SNAP SNARE 20S

    EntireName: NSF alpha-SNAP SNARE 20S
    Details: The sample was monodisperse. Some domains were disordered.
    Number of components: 3
    MassExperimental: 680 kDa / Measured by: gel permeation chromatography

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    Component #1: protein, N-ethyl Maleimide Sensitive Factor

    ProteinName: N-ethyl Maleimide Sensitive Factor / a.k.a: NSF / Oligomeric Details: hexamer / Details: 6 subunits / Number of Copies: 6 / Recombinant expression: Yes
    MassExperimental: 82.8 kDa
    SourceSpecies: Cricetulus griseus / mammal / Chinese Hamster
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Component #2: protein, Soluble NSF Attachment Protein

    ProteinName: Soluble NSF Attachment Protein / a.k.a: alpha-SNAP / Recombinant expression: Yes
    MassExperimental: 33.4 kDa
    SourceSpecies: Bos taurus / mammal / Cattle /

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    Component #3: protein, Soluble NSF Attachment Protein Receptor

    ProteinName: Soluble NSF Attachment Protein Receptor / a.k.a: SNARE / Recombinant expression: Yes
    MassExperimental: 82.3 kDa
    SourceSpecies: Unidentified / Chinese Hamster

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.2 mg/ml
    Buffer solution: 20mM HEPES, pH 7.4, 300 mM NACl, 2 mM MgCl2, 5mM b-mercaptoethanol, 0.01/0.1 mM ADP/ATP nucleotide
    pH: 7.4
    Support filmholey carbon film
    Stainingcryo (no stain)
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 80 % / Details: Vitrification instrument: Technion plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 62000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 85 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1.4 / Details: 3 x 3 averaging, final step size = 27 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 31592 / Details: manual particle selection / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionAlgorithm: Common lines / Software: IMAGIC, FREALIGN / CTF correction: FREALIGN / Resolution: 11 A / Resolution method: FSC 0.5 / Details: Final map was calculated from three data sets

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