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    Yorodumi
    - EMDB-1895: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1895
    TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
    KeywordsRibosome assembly / 30S subunit / YjeQ protein / RsgA protein / GTPase
    SampleEscherichia coli 30S ribosomal subunit in complex with the YjeQ protein
    SourceEscherichia coli / bacteria /
    Map dataYjeQ in complex with the 30S ribosomal subunit
    Methodsingle particle reconstruction, at 16.5 A resolution
    AuthorsJomaa A / Stewart G / Mears JA / Kireeva I / Brown ED / Ortega J
    CitationRNA, 2011, 17, 2026-2038

    RNA, 2011, 17, 2026-2038 StrPapers
    Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
    Ahmad Jomaa / Geordie Stewart / Jason A Mears / Inga Kireeva / Eric D Brown / Joaquin Ortega

    DateDeposition: Apr 18, 2011 / Header (metadata) release: May 27, 2011 / Map release: Oct 28, 2011 / Last update: Apr 18, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0088
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.0088
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4a2i
    • Surface level: 0.0088
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1895.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2.54 A/pix
    = 325.12 A
    128 pix
    2.54 A/pix
    = 325.12 A
    128 pix
    2.54 A/pix
    = 325.12 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.54 A
    Density
    Contour Level:0.0088 (by author), 0.0088 (movie #1):
    Minimum - Maximum-0.0217409 - 0.0623605
    Average (Standard dev.)0.000295723 (0.00440148)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin000
    Limit127127127
    Spacing128128128
    CellA=B=C: 325.12 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.542.542.54
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z325.120325.120325.120
    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/NS128128128
    D min/max/mean-0.0220.0620.000

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    Supplemental data

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    Sample components

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    Entire Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...

    EntireName: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
    Details: 30S was mixed with YjeQ in 1-to-5 molar ratio / Number of components: 2
    MassTheoretical: 900 kDa

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    Component #1: ribosome-prokaryote, 30S ribosomal subunit

    Ribosome-prokaryoteName: 30S ribosomal subunit / a.k.a: 30S subunit / Prokaryote: SSU 30S / Recombinant expression: No
    MassTheoretical: 900 kDa
    SourceSpecies: Escherichia coli / bacteria /

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    Component #2: protein, RsgA, YjeQ

    ProteinName: RsgA, YjeQ / a.k.a: Assembly factor / Oligomeric Details: Monomer / Recombinant expression: Yes
    MassExperimental: 39 kDa
    SourceSpecies: Escherichia coli / bacteria / / Strain: BW25113
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pDEST17-YjeQ
    Source (natural)Cell: Cytoplasm

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.9 mg/ml
    Buffer solution: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol.
    pH: 7.5
    Support film200 mesh copper grid
    VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: Blot for 7 seconds / Details: Vitrification instrument: FEI Vitrobot III

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F / Date: May 12, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: Corrected at 200000 times magnification / Cs: 1 mm / Imaging mode: BRIGHT FIELD / Defocus: 650 - 3900 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from -175 C to ambient
    Model: GATAN LIQUID NITROGEN / Temperature: 100 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 150 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 2.54 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 16228 / Details: Particles were picked with Boxer. / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: Xmipp / CTF correction: Each micrograph / Resolution: 16.5 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL
    Details: Protocol: Rigid Body. Each domain of YjeQ was fitted separately
    Input PDB model: 2AVY
    Modeling #2Software: Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL
    Details: Protocol: Rigid Body. Each domain of YjeQ was fitted separately
    Input PDB model: 2RCN
    Output model

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