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    - EMDB-1917: Intermediate binding positions of RRF and EF-G on the post-termin... -

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    Basic information

    Entry
    Database: EMDB / ID: 1917
    TitleIntermediate binding positions of RRF and EF-G on the post-termination complex
    KeywordsRibosome recycling factor / Elongation Factor G / T. thermophilus ribosome recycling factor / 70S / E. coli Post Termination Complex / cryo-EM
    SampleT. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
    SourceEscherichia coli / bacteria /
    Thermus thermophilus / bacteria / thermophilic
    Map dataE. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.
    Methodsingle particle reconstruction, at 9.9 A resolution
    AuthorsYokoyama T / Shaikh TR / Iwakura N / Kaji H / Kaji A / Agrawal RK
    CitationEMBO J., 2012, 31, 1836-1846

    EMBO J., 2012, 31, 1836-1846 StrPapers
    Structural insights into initial and intermediate steps of the ribosome-recycling process.
    Takeshi Yokoyama / Tanvir R Shaikh / Nobuhiro Iwakura / Hideko Kaji / Akira Kaji / Rajendra K Agrawal

    DateDeposition: Jun 29, 2011 / Header (metadata) release: Jul 15, 2011 / Map release: Apr 27, 2012 / Last update: Jun 29, 2011

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    Structure visualization

    Movie
    • Surface view with fitted model
    • Atomic models: : PDB-3j0e
    • Surface level: 272
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 272
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3j0e
    • Surface level: 272
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1917.map.gz (map file in CCP4 format, 8584 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    130 pix
    2.78 A/pix
    = 361.4 A
    130 pix
    2.78 A/pix
    = 361.4 A
    130 pix
    2.78 A/pix
    = 361.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.78 A
    Density
    Contour Level:272 (by author), 272 (movie #1):
    Minimum - Maximum-1350.87719727 - 3122.80712891
    Average (Standard dev.)40.61297226 (297.30963135)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions130130130
    Origin000
    Limit129129129
    Spacing130130130
    CellA=B=C: 361.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.782.782.78
    M x/y/z130130130
    origin x/y/z0.0000.0000.000
    length x/y/z361.400361.400361.400
    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/NS130130130
    D min/max/mean-1350.8773122.80740.613

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    Supplemental data

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    Sample components

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    Entire T. thermophilus Ribosome Recyling Factor and E. coli Elongation F...

    EntireName: T. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
    Number of components: 3 / Oligomeric State: Trimer
    MassTheoretical: 2.5 MDa

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    Component #1: ribosome-prokaryote, 70S E. coli Post-Termination Complex

    Ribosome-prokaryoteName: 70S E. coli Post-Termination Complex / a.k.a: 70S PoTC / Prokaryote: LSU 50S, SSU 30S / Recombinant expression: No
    MassTheoretical: 2.5 MDa
    SourceSpecies: Escherichia coli / bacteria /

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    Component #2: protein, Ribosome Recyling Factor

    ProteinName: Ribosome Recyling Factor / a.k.a: RRF / Recombinant expression: Yes
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic

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    Component #3: protein, Elongation Factor G

    ProteinName: Elongation Factor G / a.k.a: EF-G / Recombinant expression: Yes
    SourceSpecies: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.08 mg/ml
    Buffer solution: 50mM Tris-HCl (pH 7.5), 10mM Mg(OAc)2, 25mM KCl
    pH: 7.5
    Support film300 mesh copper grid
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / 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 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50310 X (calibrated) / Astigmatism: Objective correct at 200kX mag / Imaging mode: BRIGHT FIELD / Defocus: 400 - 4000 nm
    Specimen HolderHolder: Side entry liquid nitrogen cooled cryo holder / Model: OTHER / Temperature: 80 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 383 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 338823 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: SPIDER / CTF correction: each micrograph / Resolution: 9.9 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
    Input PDB model: 2AVY
    Modeling #2Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
    Input PDB model: 2AW4
    Modeling #3Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
    Input PDB model: 1EH1
    Output model

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