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    Yorodumi
    - EMDB-1422: Structure and composition of the Shigella flexneri "needle comple... -

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    Basic information

    Entry
    Database: EMDB / ID: 1422
    TitleStructure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
    Sampleneedle complex or basal body of the Shigella flexneri T3SS
    SourceShigella flexneri / bacteria
    Map dataBasal Body of Shigella flexneri T3SS - needle removed
    Methodsingle particle reconstruction, at 17 A resolution
    AuthorsBlocker AJ / Jouihri N / Larquet E / Gounon P / Ebel F / Parsot C / Sansonetti P / Allaoui A
    CitationMol. Microbiol., 2001, 39, 652-663

    Mol. Microbiol., 2001, 39, 652-663 StrPapers
    Structure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
    A Blocker / N Jouihri / E Larquet / P Gounon / F Ebel / C Parsot / P Sansonetti / A Allaoui

    DateDeposition: Aug 31, 2007 / Header (metadata) release: Sep 12, 2007 / Map release: Sep 12, 2007 / Last update: Aug 31, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 380
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 380
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1422.map.gz (map file in CCP4 format, 105470 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    300 pix
    2.2 A/pix
    = 660. A
    300 pix
    2.2 A/pix
    = 660. A
    300 pix
    2.2 A/pix
    = 660. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.2 A
    Density
    Contour Level:103, 380 (movie #1):
    Minimum - Maximum-257.841 - 820.019
    Average (Standard dev.)-12.8026 (115.599)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions300300300
    Origin-150-150-149
    Limit149149150
    Spacing300300300
    CellA=B=C: 660 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.22.22.2
    M x/y/z300300300
    origin x/y/z0.0000.0000.000
    length x/y/z660.000660.000660.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-150-150-149
    NX/NY/NZ300300300
    MAP C/R/S213
    start NC/NR/NS-150-150-149
    NC/NR/NS300300300
    D min/max/mean-257.841820.019-12.803

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    Supplemental data

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    Sample components

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    Entire needle complex or basal body of the Shigella flexneri T3SS

    EntireName: needle complex or basal body of the Shigella flexneri T3SS
    Oligomeric State: not yet fully determined / Number of components: 5

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    Component #1: protein, MxiH

    ProteinName: MxiH / Oligomeric Details: helical polymer / Details: none; copy number is approximative / Number of Copies: 120 / Recombinant expression: No
    MassTheoretical: 9.265 MDa / Experimental: 9.265 MDa
    SourceSpecies: Shigella flexneri / bacteria / Strain: M90T
    Source (natural)Organelle: T3SS / Location in cell: extracellular / Organ or tissue: bacterium
    External referencesInterPro: InterPro: 011841

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    Component #2: protein, MxiI

    ProteinName: MxiI / Oligomeric Details: probably helical / Details: none; Copy number is approximative / Recombinant expression: No / Number of Copies: 20
    MassTheoretical: 10.633 MDa / Experimental: 10.633 MDa
    SourceSpecies: Shigella flexneri / bacteria / Strain: M90T
    Source (natural)Organelle: T3SS / Location in cell: periplasmic / Cell: bacterium

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    Component #3: protein, MxiD

    ProteinName: MxiD / Oligomeric Details: oligomer
    Details: experimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state currently unknown
    Recombinant expression: No
    MassTheoretical: 60.749 MDa / Experimental: 63.218 MDa
    SourceSpecies: Shigella flexneri / bacteria / Strain: M90T
    Source (natural)Organelle: T3SS / Location in cell: outer membrane / Cell: bacterium
    External referencesInterPro: InterPro: 003522 / Gene Ontology: GO: 0015448

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    Component #4: protein, MxiG

    ProteinName: MxiG / Oligomeric Details: oligomer
    Details: no signal sequence cleavage in this protein; oligomeric state unknown
    Recombinant expression: No
    MassTheoretical: 43.002 MDa / Experimental: 43.002 MDa
    SourceSpecies: Shigella flexneri / bacteria / Strain: M90T
    Source (natural)Organelle: T3SS / Location in cell: inner membrane / Cell: bacterium
    External referencesGene Ontology: GO: 0005515

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    Component #5: protein, MxiJ

    ProteinName: MxiJ / Oligomeric Details: oligomer
    Details: experimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state unknown
    Recombinant expression: No
    MassTheoretical: 25.488 MDa / Experimental: 27.509 MDa
    SourceSpecies: Shigella flexneri / bacteria / Strain: M90T
    Source (natural)Organelle: T3SS / Location in cell: inner membrane / Cell: bacterium
    External referencesGene Ontology: GO: 0005515 / InterPro: InterPro: 006182

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: samples made in 50 mM Tris pH 8, 5 mM EDTA, 0.1 % v/v Triton X-100 and diluted 1:5 in 20 mM Tris pH 7.4
    pH: 7.4
    Support filmcarbon-coated glow-discharged copper grids
    Staining1% uranyl acetate pH 7.5
    VitrificationCryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM120T / Details: low-dose mode used, imaging done in 1999-2000
    Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 45000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 1200 nm
    Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 293 K ( 293 - 293 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 20 / Scanner: OTHER / Sampling size: 10 microns
    Details: Hi-Scan rotary drum microdensitometer used, final resolution was 2.2 A/pixel (not 5 A/ pixel as incorrectly stated in Materials and Methods of paper)

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 5 / Number of projections: 868
    Details: Particles selected using interactive WEB selection program
    3D reconstructionAlgorithm: single particle / Software: SPIDER / Resolution: 17 A
    Resolution method: Fourier ring correlation and differential phase residual
    Details: 1) 2D-average>iterative multireference alignment process (Boekema et al, 1986), using Ward's merging criterion until stable classes obtained; 2) 3D reconstruction> cylindrical symmetry was assumed and the final two dimensional projection converted to a three-dimensional map using an iterative back projection procedure (Frank, 1996).

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