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    Yorodumi
    - EMDB-5009: A cryo-EM map of the FimD-tip complex, a bacterial surface pilus ... -

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    Basic information

    Entry
    Database: EMDB / ID: 5009
    TitleA cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.
    Keywordscryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis
    SampleFimD-tip complex
    SourceEscherichia coli / bacteria /
    Map data3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
    Methodsingle particle reconstruction, at 23 A resolution
    AuthorsTang C / Thanassi D / Li H
    CitationCell, 2008, 133, 640-652

    Cell, 2008, 133, 640-652 StrPapers
    Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
    Han Remaut / Chunyan Tang / Nadine S Henderson / Jerome S Pinkner / Tao Wang / Scott J Hultgren / David G Thanassi / Gabriel Waksman / Huilin Li

    DateDeposition: Mar 14, 2008 / Header (metadata) release: Mar 21, 2008 / Map release: Apr 22, 2009 / Last update: Mar 14, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2.33535264
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 2.33535264
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5009.map.gz (map file in CCP4 format, 3457 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    96 pix
    2.54 A/pix
    = 241.3 A
    96 pix
    2.54 A/pix
    = 241.3 A
    96 pix
    2.54 A/pix
    = 241.3 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.54 A
    Density
    Contour Level:1.74, 2.3353526 (movie #1):
    Minimum - Maximum-4.68613 - 8.0905
    Average (Standard dev.)6.58932e-09 (0.871601)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions969696
    Origin-48-48-48
    Limit474747
    Spacing969696
    CellA=B=C: 241.3 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.542.542.54
    M x/y/z959595
    origin x/y/z0.0000.0000.000
    length x/y/z241.300241.300241.300
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-127-127-127
    NX/NY/NZ255255255
    MAP C/R/S123
    start NC/NR/NS-48-48-48
    NC/NR/NS969696
    D min/max/mean-4.6868.0910.000

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    Supplemental data

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    Sample components

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    Entire FimD-tip complex

    EntireName: FimD-tip complex / Details: The sample was monodisperse / Number of components: 5
    Oligomeric State: FimD usher dimer in complex with one copy each of FimH, FimF, FimG pilins and FimC chaperone
    MassTheoretical: 260 kDa / Experimental: 260 kDa

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    Component #1: cellular-component, FimD-tip complex

    Cellular-componentName: FimD-tip complex / a.k.a: Pilus assembly usher / Oligomeric Details: Dimer / Details: This component forms a dimer in the complex / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 96 kDa / Experimental: 96 kDa
    SourceSpecies: Escherichia coli / bacteria /
    Source (engineered)Expression System: Escherichia coli b strain tuner (novagen) / bacteria / image: Escherichia coli
    Vector: Tuner/pAN2 and pNH237
    Source (natural)Location in cell: Outer membrane
    External referencesGene Ontology: GO: 0015473 / InterPro: InterPro: 000015

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.04 mg/ml
    Buffer solution: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
    pH: 8
    Support filmglow-discharged lacey carbon grid
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 108 K / Humidity: 85 % / Method: 6 seconds blot
    Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F / Date: Feb 1, 2007
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Astigmatism: correction at 250,000 mag / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 5000 nm
    Specimen HolderHolder: Gatan 626 cryo holder / Model: GATAN LIQUID NITROGEN / Temperature: 103 K ( 100 - 105 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 12.7 microns / Bit depth: 14 / OD range: 1.3

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 100 / Number of projections: 11000 / Details: particles were manually selected / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Cross-common lines / Software: EMAN, SPIDER / CTF correction: Each films / Resolution: 23 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
    Details: Protocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera
    Input PDB model: 1QUN
    Chain ID: 1QUN_A

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