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    Yorodumi
    - EMDB-1366: Locking and unlocking of ribosomal motions. -

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    Basic information

    Entry
    Database: EMDB / ID: 1366
    TitleLocking and unlocking of ribosomal motions.
    SampleEF-G bound Release Complex in the presence of Puromycin and GTP
    SourceEscherichia coli / bacteria /
    Synthetic construct
    Map dataCryo-EM map of E.coli 70S ribosome
    Methodsingle particle reconstruction, at 12.8 A resolution
    AuthorsMikel V / Andrey Z / Sengupta J / Rawat U / Ehrenberg M / Frank J
    CitationCell, 2003, 114, 123-134

    Cell, 2003, 114, 123-134 StrPapers
    Locking and unlocking of ribosomal motions.
    Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank

    DateDeposition: May 22, 2007 / Header (metadata) release: May 24, 2007 / Map release: May 24, 2007 / Last update: May 22, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 30
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 30
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-1pn6
    • Surface level: 30
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1366.map.gz (map file in CCP4 format, 8584 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.82 A
    Density
    Contour Level:57.3, 30 (movie #1):
    Minimum - Maximum-118.471 - 239.101
    Average (Standard dev.)2.85556 (25.5653)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions130130130
    Origin-65-65-65
    Limit646464
    Spacing130130130
    CellA=B=C: 366.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.822.822.82
    M x/y/z130130130
    origin x/y/z0.0000.0000.000
    length x/y/z366.600366.600366.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS-65-65-65
    NC/NR/NS130130130
    D min/max/mean-118.471239.1012.856

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    Supplemental data

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    Sample components

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    Entire EF-G bound Release Complex in the presence of Puromycin and GTP

    EntireName: EF-G bound Release Complex in the presence of Puromycin and GTP
    Number of components: 4

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    Component #1: ribosome-prokaryote, Release Complex

    Ribosome-prokaryoteName: Release Complex / Details: mRNA, tRNA / Prokaryote: ALL / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria / / Strain: MRE600

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    Component #2: ligand, Puromycin

    LigandName: Puromycin / Details: Antibiotic / Recombinant expression: No
    SourceSpecies: Synthetic construct

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    Component #3: ligand, EF-G

    LigandName: EF-G / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria / / Strain: MRE600

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    Component #4: ligand, GTP

    LigandName: GTP / Recombinant expression: No
    SourceSpecies: Synthetic construct

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Jul 11, 2003
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 1 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Back projection / Software: SPIDER, package / CTF correction: CTF correctionn of 3D map / Resolution: 12.8 A / Resolution method: FSC 0.5

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    Output model

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