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    - EMDB-1882: Mutually-induced conformational switching of RNA and coat protein... -

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    Basic information

    Entry
    Database: EMDB / ID: 1882
    TitleMutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
    KeywordsBacteriophage MS2 / virus assembly / quasi-equivalence / ssRNA virus
    SampleBacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
    SourceEnterobacterio phage MS2 / virus / MS2
    Enterobacteria phage MS2 / virus / MS2
    Map dataThis is a surface-rendered view of a Bacteriophage MS2 virus-like particle composed of purified coat protein and genomic RNA
    Methodsingle particle (icosahedral) reconstruction, at 32 A resolution
    AuthorsRolfsson O / Toropova K / Ranson NA / Stockley PG
    CitationJ. Mol. Biol., 2010, 401, 309-322

    J. Mol. Biol., 2010, 401, 309-322 StrPapers
    Mutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
    Ottar Rolfsson / Katerina Toropova / Neil A Ranson / Peter G Stockley

    DateDeposition: Feb 21, 2011 / Header (metadata) release: May 13, 2011 / Map release: May 13, 2011 / Last update: Feb 21, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1882.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    1.87 A/pix
    = 374. A
    200 pix
    1.87 A/pix
    = 374. A
    200 pix
    1.87 A/pix
    = 374. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.87 A
    Density
    Contour Level:1 (by emdb), 1 (movie #1):
    Minimum - Maximum-4.45316 - 5.72175
    Average (Standard dev.)5.57511e-09 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin000
    Limit199199199
    Spacing200200200
    CellA=B=C: 374 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.871.871.87
    M x/y/z200200200
    origin x/y/z-0.000-0.000-0.000
    length x/y/z374.000374.000374.000
    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/NS200200200
    D min/max/mean-4.4535.7220.000

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    Supplemental data

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    Sample components

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    Entire Bacteriophage MS2 virus-like particles assembled in vitro from pu...

    EntireName: Bacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
    Number of components: 2 / Oligomeric State: One capsid to one RNA

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    Component #1: virus, Enterobacterio phage MS2

    VirusName: Enterobacterio phage MS2 / a.k.a: MS2 / Class: VIRUS-LIKE PARTICLE / Enveloped: No / Empty: No / Isolate: STRAIN
    SpeciesSpecies: Enterobacterio phage MS2 / virus / MS2
    Source (natural)Host Species: Escherichia coli / bacteria / / Host category: BACTERIA(EUBACTERIA)

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    Component #2: nucleic-acid, Single stranded RNA MS2 genome

    Nucleic-acidName: Single stranded RNA MS2 genome / a.k.a: Single stranded RNA MS2 genome / Class: RNA
    Details: Single stranded RNA MS2 genome was phenol-chloroform extracted from wild type MS2 phage
    Structure: SINGLE STRANDED / Synthetic: No
    SourceSpecies: Enterobacteria phage MS2 / virus / MS2

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 50mM Tris-acetate, 1mM magnesium acetate, 40mM ammonium acetate
    pH: 7.6
    Support filmQuantifoil R2/1 200 mesh holly carbon grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: 1.6s blot
    Details: Vitrification instrument: Double-sided custom pneumatic blotter

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 52750 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Side entry / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: OTHER / Sampling size: 9.88 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 80 / Number of class averages: 19 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Projection matching / Software: Spider / CTF correction: Phase flip each particle / Resolution: 32 A / Resolution method: FSC 0.5

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