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    Yorodumi
    - EMDB-5352: Structure of a type III secretion needle -

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    Basic information

    Entry
    Database: EMDB / ID: 5352
    TitleStructure of a type III secretion needle
    Keywordstype III secretion system / needle / helical filament
    SampleShigella needle
    SourceShigella flexneri / bacteria
    Map dataThis is an reconstruction of the type III secretion needle
    Methodhelical reconstruction, at 7.7 A resolution
    AuthorsFujii T / Cheung M / Blanco A / Kato T / Blocker AJ / Namba K
    CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 4461-4466

    Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 4461-4466 StrPapers
    Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms.
    Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba

    DateDeposition: Nov 2, 2011 / Header (metadata) release: Nov 28, 2011 / Map release: Feb 20, 2012 / Last update: Nov 2, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3j0r
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3j0r
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-2mme
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-2mme
    • Surface level: 6.76
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

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    Map

    Fileemd_5352.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    1.68 A/pix
    = 168. A
    100 pix
    1.68 A/pix
    = 168. A
    100 pix
    1.68 A/pix
    = 168. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.68 A
    Density
    Contour Level:6.76 (by author), 6.76 (movie #1):
    Minimum - Maximum-11.36894798 - 22.53497505
    Average (Standard dev.)0.10644222 (2.6820209)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin-50-50-50
    Limit494949
    Spacing100100100
    CellA=B=C: 168 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.681.681.68
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z168.000168.000168.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-50-50-50
    NC/NR/NS100100100
    D min/max/mean-11.36922.5350.106

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    Supplemental data

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    Sample components

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    Entire Shigella needle

    EntireName: Shigella needle / Number of components: 1 / Oligomeric State: helical assembly of MxiH

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    Component #1: protein, MxiH

    ProteinName: MxiH / a.k.a: MxiH / Recombinant expression: Yes
    SourceSpecies: Shigella flexneri / bacteria

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: RIGHT HANDED / Delta z: 4.3 A / Delta phi: 64.06 deg.
    Sample solutionBuffer solution: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 / pH: 7.4
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 3.5 seconds before plunging / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3200FSC / Date: Jul 2, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 89285 X (calibrated) / Cs: 1.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm / Energy filter: JEOL Omega filter / Energy window: 0-10 eV
    Specimen HolderHolder: top entry / Model: OTHER / Temperature: 50 K ( 50 - 60 K)
    CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 330 / Sampling size: 15 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: Projection Matching / Software: SPIDER / CTF correction: CTFFIND3 Each particle / Resolution: 7.7 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Output model

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