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    Yorodumi
    - EMDB-1900: Cryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex -

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    Basic information

    Entry
    Database: EMDB / ID: 1900
    TitleCryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex
    KeywordsBacteriophage / SPP1 / Tail tip / gp19.1 / Dit / gp21 / Tal / tail adsorption apparatus / infection mechanism
    SampleSPP1 bacteriophage gp19.1-gp21(1-552) complex
    Sourceunidentified phage / virus / Dit, Tal
    Map dataCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
    Methodsingle particle reconstruction, at 26 A resolution
    AuthorsGoulet A / Lai-Kee-Him J / Veesler D / Auzat I / Robin G / Shepherd DA / Ashcroft AE / Richard E / Lichiere J / Tavares P / Cambillau C / Bron P
    CitationJ. Biol. Chem., 2011, 286, 25397-25405

    J. Biol. Chem., 2011, 286, 25397-25405 StrPapers
    The opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages.
    Adeline Goulet / Joséphine Lai-Kee-Him / David Veesler / Isabelle Auzat / Gautier Robin / Dale A Shepherd / Alison E Ashcroft / Eric Richard / Julie Lichière / Paulo Tavares / Christian Cambillau / Patrick Bron

    DateDeposition: May 24, 2011 / Header (metadata) release: May 27, 2011 / Map release: Jun 10, 2011 / Last update: May 24, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 60
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 60
    • Imaged by UCSF CHIMERA
    • Download
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    Map

    Fileemd_1900.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    4.38 A/pix
    = 438. A
    100 pix
    4.38 A/pix
    = 438. A
    100 pix
    4.38 A/pix
    = 438. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.38 A
    Density
    Contour Level:60 (by author), 60 (movie #1):
    Minimum - Maximum0 - 100
    Average (Standard dev.)51.7892 (3.06874)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin-49-50-50
    Limit504949
    Spacing100100100
    CellA=B=C: 438 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.384.384.38
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z438.000438.000438.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS-50-49-50
    NC/NR/NS100100100
    D min/max/mean0.000100.00051.789

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    Supplemental data

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    Sample components

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    Entire SPP1 bacteriophage gp19.1-gp21(1-552) complex

    EntireName: SPP1 bacteriophage gp19.1-gp21(1-552) complex / Number of components: 2
    Oligomeric State: This complex assembles two back-to- back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack
    MassExperimental: 730 kDa / Measured by: SEC, MALS, RI, UV, QELS

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    Component #1: protein, gp19.1

    ProteinName: gp19.1 / a.k.a: Dit / Recombinant expression: Yes
    SourceSpecies: unidentified phage / virus / Dit

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    Component #2: protein, gp21(1-552)

    ProteinName: gp21(1-552) / a.k.a: Tal / Recombinant expression: Yes
    SourceSpecies: unidentified phage / virus / Tal

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.07 mg/ml / Buffer solution: 10 mM HEPES, 150 mM NaCl / pH: 7.5
    Support filmQuantifoil R 2/2 grids
    VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 102.15 K / Humidity: 90 % / Method: Blot for 2s, both sides / Details: Vitrification instrument: Cryoplunge CP3 gatan

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2200FS / Details: Images recorded on a JEOL 2200FS
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 45591 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2500 nm / Energy filter: Omega JEOL / Energy window: 0-20 eV
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC / Temperature: 98.15 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 10 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 15171 / Applied symmetry: D3 (2*3 fold dihedral)
    3D reconstructionAlgorithm: Projection matching / Software: IMAGIC / CTF correction: Each particle / Resolution: 26 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement protocol: rigid body / Refinement space: REAL
    Details: The initial fit was done by manual docking followed by refinement using the (fit in map) Chimera plugging
    Input PDB model: 2X8K

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