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    - EMDB-1641: Helical reconstruction of the bacterial L-type flagella filament -

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    Basic information

    Entry
    Database: EMDB / ID: 1641
    TitleHelical reconstruction of the bacterial L-type flagella filament
    Keywordsbacterial flagellum
    SampleS. enterica serovar Typhimurium L-type flagella filament
    SourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
    Map dataThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
    Methodhelical reconstruction, at 4 A resolution
    AuthorsMaki-Yonekura S / Yonekura K / Namba K
    CitationNat. Struct. Mol. Biol., 2010, 17, 417-422

    Nat. Struct. Mol. Biol., 2010, 17, 417-422 StrPapers
    Conformational change of flagellin for polymorphic supercoiling of the flagellar filament.
    Saori Maki-Yonekura / Koji Yonekura / Keiichi Namba

    DateDeposition: Aug 12, 2009 / Header (metadata) release: Jan 26, 2010 / Map release: Aug 19, 2011 / Last update: Aug 12, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 550
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 550
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3a5x
    • Surface level: 550
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1641.map.gz (map file in CCP4 format, 33525 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    251 pix
    1 A/pix
    = 251. A
    131 pix
    1 A/pix
    = 261. A
    261 pix
    1 A/pix
    = 131. 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:550 (by author), 550 (movie #1):
    Minimum - Maximum-948.453 - 2134.49
    Average (Standard dev.)4.55795 (60.6009)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions131261251
    Origin000
    Limit130260250
    Spacing131261251
    CellA: 131 A / B: 261 A / C: 251 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z111
    M x/y/z131261251
    origin x/y/z0.0000.0000.000
    length x/y/z131.000261.000251.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS261131251
    D min/max/mean-948.4532134.4914.558

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    Supplemental data

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    Sample components

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    Entire S. enterica serovar Typhimurium L-type flagella filament

    EntireName: S. enterica serovar Typhimurium L-type flagella filament
    Number of components: 1

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    Component #1: protein, Flagella filament

    ProteinName: Flagella filament / a.k.a: Flagella filament / Oligomeric Details: Helical assembly / Recombinant expression: No
    SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / bacteria
    Strain: SJW1660
    Source (natural)Location in cell: Outside cell

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3000SFF
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Top entry / Model: JEOL / Temperature: 4 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: OTHER / Sampling size: 5 microns

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: Helical reconstruction / Software: Handmade / CTF correction: Each filament / Resolution: 4 A / Resolution method: Figure of merit

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    Atomic model buiding

    Output model

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