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    - PDB-1ucu: R-type straight flagellar filament made of full-length flagellin -

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    Basic information

    Entry
    Database: PDB / ID: 1ucu
    TitleR-type straight flagellar filament made of full-length flagellin
    DescriptorFlagellin
    KeywordsStructural protein / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION
    Specimen sourceSalmonella typhimurium / bacteria
    MethodElectron microscopy (4 A resolution / Helical / Vitreous ice (cryo EM))
    AuthorsYonekura, K. / Maki-Yonekura, S. / Namba, K.
    CitationNature, 2003, 424, 643-650

    primary. Nature, 2003, 424, 643-650 StrPapers
    Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
    Koji Yonekura / Saori Maki-Yonekura / Keiichi Namba

    #1. NATURE, 2001, 410, 331-337
    Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling
    Samatey, F.A. / Imada, K. / Nagashima, S. / Vonderviszt, F. / Kumasaka, T. / Yamamoto, M. / Namba, K.

    DateDeposition: Apr 22, 2003 / Release: Aug 12, 2003 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    A: phase 1 Flagellin

    51.6 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    51,5521
    Polyers51,5521
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / phase 1 Flagellin / Mutation: A449V / Source: Salmonella typhimurium (gene. exp.) / References: UniProt: P06179

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: R-TYPE STRAIGHT FLAGELLAR FILAMENT / Aggregation state: FILAMENT
    Buffer solutionName: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
    Sample preparationpH: 7.8 / Sample conc.: 0.1 mg/ml
    Specimen supportDetails: QUANTIFOIL R1.2/1.3 (25 NM THICK)

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    Electron microscopy imaging

    MicroscopyMicroscope model: JEOL JEM-3000SFF
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2000 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 47600 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 1.6 mm
    Specimen holderTemperature: 4 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM

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    Processing

    SoftwareName: FEX-PLOR / Classification: refinement
    ComputingStructure refinement: FX-PLOR
    Image selectionSoftware name: FEX-PLOR / Number of particles: 102
    3D reconstructionMethod: HELICAL RECONSTRUCTION / Resolution: 4 A / Nominal pixel size: 1 A/pix / Actual pixel size: 1.05 A/pix
    Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT
    CTF correction method: BOTH AMPLITUDE AND PHASE
    Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated.
    Atomic model buildingRef protocol: POSITIONAL AND SIMULATED ANNEALING / Ref space: RECIPROCAL / Target criteria: amplitude-weighted phase residual
    Least-squares processR factor R work: 0.3 / Highest resolution: 4 A / Lowest resolution: 30 A
    Refine hist #LASTHighest resolution: 4 A / Lowest resolution: 30 A
    Number of atoms included #LASTProtein: 3617 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3617

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