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    - EMDB-5125: PSRP1 is not a bona fide ribosomal protein, but a stress response... -

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    Basic information

    Entry
    Database: EMDB / ID: 5125
    TitlePSRP1 is not a bona fide ribosomal protein, but a stress response factor
    Keywords70S / E.coli Ribosome / Cryo-EM PSRP1 / PSRP-1 / ribosomal protein / stress response factor.
    Sample70S E.coli ribosome with PSRP1 in vitro
    SourceEscherichia coli / bacteria /
    Spinacia oleracea / plant / spinach / Spinach
    Map data70S E.coli Ribosome with PSRP1, in vitro
    Methodsingle particle reconstruction, at 9.8 A resolution
    AuthorsSharma MR / Donhofer A / Barat C / Datta P / Fucini P / Wilson DN / Agrawal RK
    CitationJ. Biol. Chem., 2010, 285, 4006-4014

    J. Biol. Chem., 2010, 285, 4006-4014 StrPapers
    PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
    Manjuli R Sharma / Alexandra Dönhöfer / Chandana Barat / Viter Marquez / Partha P Datta / Paola Fucini / Daniel N Wilson / Rajendra K Agrawal

    DateDeposition: Jul 21, 2009 / Header (metadata) release: May 5, 2010 / Map release: May 5, 2010 / Last update: Jul 21, 2009

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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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    Supplemental images

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    Map

    Fileemd_5125.map.gz (map file in CCP4 format, 8584 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    130 pix
    2.76 A/pix
    = 358.8 A
    130 pix
    2.76 A/pix
    = 358.8 A
    130 pix
    2.76 A/pix
    = 358.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.76 A
    Density
    Contour Level:30 (by author), 30 (movie #1):
    Minimum - Maximum-120.19511414 - 276.03640747
    Average (Standard dev.)2.53906465 (27.40571404)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions130130130
    Origin000
    Limit129129129
    Spacing130130130
    CellA=B=C: 358.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.762.762.76
    M x/y/z130130130
    origin x/y/z0.0000.0000.000
    length x/y/z358.800358.800358.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS130130130
    D min/max/mean-120.195276.0362.539

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    Supplemental data

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    Sample components

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    Entire 70S E.coli ribosome with PSRP1 in vitro

    EntireName: 70S E.coli ribosome with PSRP1 in vitro / Number of components: 2
    MassTheoretical: 2.8 MDa / Experimental: 2.8 MDa

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    Component #1: ribosome-prokaryote, 70S Ribosome

    Ribosome-prokaryoteName: 70S Ribosome / Prokaryote: LSU 50S, SSU 30S / Recombinant expression: No
    MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa
    SourceSpecies: Escherichia coli / bacteria /

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    Component #2: ligand, plastid specific ribosomal protein-1

    LigandName: plastid specific ribosomal protein-1 / a.k.a: PSRP1 / Recombinant expression: No
    MassTheoretical: 270 kDa / Experimental: 270 kDa
    SourceSpecies: Spinacia oleracea / plant / spinach / Spinach
    Source (natural)Organelle: Chloroplast

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 20mM Hepes-KOH, 8.2mM MgCl2, 80mM NH4Cl, 4mM beta-mercaptoethanol
    pH: 7.6
    Support film300 mesh coper grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Method: Blot for 3 seconds then plunge / Details: Vitrification instrument: Plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50760 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4200 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 53 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 18 / Applied symmetry: C1 (asymmetric) / Number of projections: 32611
    3D reconstructionAlgorithm: projection matching / Software: Spider / CTF correction: Each Micrograph / Resolution: 9.8 A / Resolution method: FSC 0.5

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