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    Yorodumi
    - EMDB-5035: Structure of a type IV secretion system core complex -

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    Basic information

    Entry
    Database: EMDB / ID: 5035
    TitleStructure of a type IV secretion system core complex
    Keywordsbacterial secretion / type IV secretion / vir / tra
    SampletraN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
    Map datavolume
    Methodsingle particle reconstruction, at 18 A resolution
    AuthorsFronzes R / Schafer E / Wang L / Saibil H / Orlova E / Waksman G
    CitationScience, 2009, 323, 266-268

    Science, 2009, 323, 266-268 StrPapers
    Structure of a type IV secretion system core complex.
    Rémi Fronzes / Eva Schäfer / Luchun Wang / Helen R Saibil / Elena V Orlova / Gabriel Waksman

    DateDeposition: Nov 10, 2008 / Header (metadata) release: Nov 18, 2008 / Map release: Apr 15, 2009 / Last update: Nov 10, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.025
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.025
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5035.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    2.5 A/pix
    = 500. A
    200 pix
    2.5 A/pix
    = 500. A
    200 pix
    2.5 A/pix
    = 500. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.5 A
    Density
    Contour Level:0.025, 0.025 (movie #1):
    Minimum - Maximum-0.384705 - 0.385275
    Average (Standard dev.)0.000218033 (0.0162388)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin000
    Limit199199199
    Spacing200200200
    CellA=B=C: 500 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.52.52.5
    M x/y/z200200200
    origin x/y/z0.0000.0000.000
    length x/y/z500.000500.000500.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-127-127-127
    NX/NY/NZ255255255
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS200200200
    D min/max/mean-0.3850.3850.000

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    Supplemental data

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    Sample components

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    Entire traN/traO/traF encoded by pKM101. traN is mutated to replace cys1...

    EntireName: traN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
    Details: aggregates a high concentration / Number of components: 3 / Oligomeric State: 14
    MassTheoretical: 1.05 MDa / Experimental: 1.1 MDa / Measured by: gel filtration

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    Component #1: protein, traF

    ProteinName: traF / a.k.a: traF / Oligomeric Details: 14-mer / Number of Copies: 14 / Recombinant expression: Yes
    MassTheoretical: 40 kDa
    SourceStrain: BL21
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK-IBA3c
    Source (natural)Location in cell: inner membrane / Cell: Escherichia coli

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    Component #2: protein, traO

    ProteinName: traO / a.k.a: traO / Oligomeric Details: 14-mer / Recombinant expression: Yes / Number of Copies: 14
    MassTheoretical: 30 kDa
    SourceStrain: BL21
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK-IBA3c
    Source (natural)Location in cell: outer membrane / Cell: Escherichia coli

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    Component #3: protein, traO

    ProteinName: traO / a.k.a: traO / Oligomeric Details: 14-mer / Details: non lipidated subunit / Number of Copies: 14 / Recombinant expression: Yes
    MassTheoretical: 5 kDa
    SourceStrain: BL21
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK-IBA3c
    Source (natural)Location in cell: outer membrane / Cell: Escherichia coli

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.5 mg/ml / Buffer solution: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
    Support filmcarbon coated copper grids
    Staining2% uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Jan 1, 2008
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 42000 X (nominal), 42000 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm
    Specimen HolderHolder: side entry room temperature / Model: OTHER / Temperature: 293 K ( 293 - 293 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 2

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 300 / Number of projections: 1231 / Applied symmetry: C14 (14 fold cyclic)
    3D reconstructionAlgorithm: common lines / Software: imagic / Details: final map was calculated from 300 class averages / Resolution: 18 A / Resolution method: FSC 0.5

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