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    Yorodumi
    - EMDB-1924: Ribosome Assembly Factors Prevent Premature Translation Initiatio... -

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    Basic information

    Entry
    Database: EMDB / ID: 1924
    TitleRibosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates
    Keywordspre-40S / 40S intermediate / Ltv1 deletion
    SampleS. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
    SourceSaccharomyces cerevisiae / yeast / Bakers' yeast /
    Map dataSurface rendered Ltv1 deletion map
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsStrunk BS / Loucks CR / Su M / Vashisth H / Cheng S / Schilling J / BrooksIII CL / Karbstein K / Skiniotis G
    CitationScience, 2011, 333, 1449-1453

    Science, 2011, 333, 1449-1453 StrPapers
    Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.
    Bethany S Strunk / Cherisse R Loucks / Min Su / Harish Vashisth / Shanshan Cheng / Justin Schilling / Charles L Brooks / Katrin Karbstein / Georgios Skiniotis

    DateDeposition: Jul 5, 2011 / Header (metadata) release: Nov 4, 2011 / Map release: Nov 4, 2011 / Last update: Jul 5, 2011

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    Structure visualization

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    • Surface view with section colored by density value
    • Surface level: 0.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.5
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1924.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    2.24 A/pix
    = 358.4 A
    160 pix
    2.24 A/pix
    = 358.4 A
    160 pix
    2.24 A/pix
    = 358.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.24 A
    Density
    Contour Level:0.3 (by author), 0.5 (movie #1):
    Minimum - Maximum-2.1019 - 3.94117
    Average (Standard dev.)0.0028384 (0.359594)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin000
    Limit159159159
    Spacing160160160
    CellA=B=C: 358.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.242.242.24
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z358.400358.400358.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS160160160
    D min/max/mean-2.1023.9410.003

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    Supplemental data

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    Sample components

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    Entire S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion

    EntireName: S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
    Details: Monodisperse / Number of components: 1
    MassTheoretical: 1.4 MDa

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    Component #1: ribosome-eukaryote, pre-40S

    Ribosome-eukaryoteName: pre-40S / a.k.a: pre-40S / Eukaryote: SSU 40S / Recombinant expression: No
    MassTheoretical: 1.4 MDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Bakers' yeast /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1.5 mg/ml
    Buffer solution: 50mM Tris-Cl, 100mM NaCl, 10mM MgCl2, 0.075% NP40, 1mM imidazole, 2mM EGTA, 10 mM BME
    pH: 7.5
    Support filmQuantifoil
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 100 % / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 66964 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4000 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: OTHER / Temperature: 89 K ( 89 - 89 K)
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 350 / Sampling size: 2.24 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 10235 / Details: Manual particle selection / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Euler angles: EMAN convention / Software: EMAN / CTF correction: Each micrograph / Details: Final map was filtered to 20A resolution / Resolution: 20 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: NAMD / Refinement protocol: flexible / Target criteria: CC / Refinement space: REAL / Details: Protocol: MDFF
    Input PDB model: 3O2Z

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