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    Yorodumi
    - EMDB-1327: Reconfiguration of yeast 40S ribosomal subunit domains by the tra... -

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    Basic information

    Entry
    Database: EMDB / ID: 1327
    TitleReconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
    SampleEukaryotic translation preinitiation complex 43S
    SourceSaccharomyces cerevisiae / yeast / Baker's yeast /
    Map dataReconstruction of the 43S preinitiation complex from S. cerevisiae.
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsGilbert RJC / Gordiyenko Y / von der Haar T / Sonnen AF-P / Hoffman GW / Nardelli M / Stuart DI / McCarthy JEG
    CitationProc. Natl. Acad. Sci. U.S.A., 2007, 104, 5788-5793

    Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 5788-5793 StrPapers
    Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
    Robert J C Gilbert / Yulya Gordiyenko / Tobias von der Haar / Andreas F-P Sonnen / Gregor Hofmann / Maria Nardelli / David I Stuart / John E G McCarthy

    DateDeposition: Mar 6, 2007 / Header (metadata) release: Mar 6, 2007 / Map release: Apr 6, 2007 / Last update: Mar 6, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 22.408501399
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 22.408501399
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1327.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesY (Sec.)X (Row.)Z (Col.)
    128 pix
    3.33 A/pix
    = 426.24 A
    128 pix
    3.33 A/pix
    = 426.24 A
    128 pix
    3.33 A/pix
    = 426.24 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.33 A
    Density
    Contour Level:21.7, 22.4085014 (movie #1):
    Minimum - Maximum-97.4 - 200
    Average (Standard dev.)1.93102 (13.2256)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderZXY
    Dimensions128128128
    Origin-64-64-64
    Limit636363
    Spacing128128128
    CellA=B=C: 426.24 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.333.333.33
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z426.240426.240426.240
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S312
    start NC/NR/NS-64-64-64
    NC/NR/NS128128128
    D min/max/mean-97.400200.0001.931

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    Supplemental data

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    Sample components

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    Entire Eukaryotic translation preinitiation complex 43S

    EntireName: Eukaryotic translation preinitiation complex 43S / Oligomeric State: 40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A / Number of components: 6
    MassTheoretical: 1.941 MDa

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    Component #1: ribosome-eukaryote, Small subunit

    Ribosome-eukaryoteName: Small subunit / a.k.a: 40S / Details: S. cerevisiae / Eukaryote: SSU 40S / Recombinant expression: No
    MassTheoretical: 1.4 MDa / Experimental: 1.4 MDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /

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    Component #2: nucleic-acid, tRNA

    Nucleic-acidName: tRNA / Class: T-RNA / Structure: DOUBLE HELIX / Synthetic: No
    MassTheoretical: 23 kDa / Experimental: 23 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /

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    Component #3: protein, eukaryotic translation initiation factor 2

    ProteinName: eukaryotic translation initiation factor 2 / a.k.a: eIF2 / Oligomeric Details: heterotrimer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 124 kDa / Experimental: 124 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast /
    Source (natural)Location in cell: Cytosol

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    Component #4: protein, eukaryotic translation initiation factor 3

    ProteinName: eukaryotic translation initiation factor 3 / a.k.a: eIF3 / Oligomeric Details: Heteropentamer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 362 kDa / Experimental: 362 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast /
    Source (natural)Location in cell: Cytosol

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    Component #5: protein, eukaryotic translation initiation factor 1

    ProteinName: eukaryotic translation initiation factor 1 / a.k.a: eIF1 / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 12 kDa / Experimental: 12 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast /
    Source (natural)Location in cell: Cytosol

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    Component #6: protein, eukaryotic translation initiation factor 1A

    ProteinName: eukaryotic translation initiation factor 1A / a.k.a: eIF1A / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 17 kDa / Experimental: 17 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast /
    Source (natural)Location in cell: Cytosol

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP
    pH: 7.4
    Support film300 mesh copper grid with lacey carbon film
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
    Method: Blot with Whatman number 1 paper for 1-2 seconds prior to plunging.
    Details: Vitrification instrument: Home-made plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Astigmatism: Astigmatism corrected at 100,000 x / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2055 - 11685 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 70 / Scanner: OTHER / Sampling size: 8.33 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 27101 / Details: The particles were selected manually. / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Single particle / Software: IMAGIC, EMAN, FREALIGN, SPIDER, GAP / CTF correction: Per micrograph / Resolution: 20 A / Resolution method: FSC 0.5 / Euler angles: SPIDER Euler angle convention
    Details: Final maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure.

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    Atomic model buiding

    Modeling #1Software: GAP / Refinement protocol: rigid body / Target criteria: Real space CC and R-factor / Refinement space: REAL / Details: Protocol: Rigid body

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