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    Yorodumi
    - EMDB-5144: Ab initio reconstruction of a poliovirus-receptor complex via the... -

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    Basic information

    Entry
    Database: EMDB / ID: 5144
    TitleAb initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method
    Keywordsrandom-model method / ab initio reconstruction / poliovirus-receptor complex.
    SamplePoliovirus-receptor complex
    SourceHuman enterovirus C / virus / Poliovirus
    Map dataPoliovirus-receptor complex
    Methodsingle particle reconstruction, at 30 A resolution
    AuthorsSanz E / Stewart AB / Belnap DM
    CitationJ. Struct. Biol., 2010, 171, 216-222

    primary. J. Struct. Biol., 2010, 171, 216-222 StrPapers
    The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.
    Eduardo Sanz-García / Aaron B Stewart / David M Belnap

    1. PROC.NAT.ACAD.SCI.USA, 2000, 97, 73-78
    Three-dimensional structure of poliovirus receptor bound to poliovirus
    Belnap DM / McDermott BM Jr / Filman DJ / Cheng N / Trus BL / Zuccola HJ / Racaniello VR / Hogle JM / Steven AC

    DateDeposition: Nov 21, 2009 / Header (metadata) release: Apr 26, 2010 / Map release: Apr 26, 2010 / Last update: Nov 21, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.631
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.631
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5144.map.gz (map file in CCP4 format, 92345 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    287 pix
    1.84 A/pix
    = 528.08 A
    287 pix
    1.84 A/pix
    = 528.08 A
    287 pix
    1.84 A/pix
    = 528.08 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.84 A
    Density
    Contour Level:0.631 (by author), 0.631 (movie #1):
    Minimum - Maximum-1.78653 - 2.201
    Average (Standard dev.)0.0187361 (0.283488)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions287287287
    Origin-143-143-143
    Limit143143143
    Spacing287287287
    CellA=B=C: 528.08 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.841.841.84
    M x/y/z287287287
    origin x/y/z0.0000.0000.000
    length x/y/z528.080528.080528.080
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-143-143-143
    NC/NR/NS287287287
    D min/max/mean-1.7872.2010.019

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    Supplemental data

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    Sample components

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    Entire Poliovirus-receptor complex

    EntireName: Poliovirus-receptor complex
    Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
    Number of components: 2 / Oligomeric State: 1 virus binds 60 receptors

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    Component #1: virus, Human enterovirus C

    VirusName: Human enterovirus C / a.k.a: Poliovirus / Class: VIRION
    Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
    Empty: No / Enveloped: No / Isolate: SEROTYPE
    SpeciesSpecies: Human enterovirus C / virus / Poliovirus
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
    Shell #1Name of element: VP1 VP2 VP3 / Diameter: 242 A / T number(triangulation number): 1

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 38000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2600 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
    CameraDetector: GENERIC FILM

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    Image acquisition

    Image acquisitionDetails: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 5626
    Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
    Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: PFT3DR, Bsoft / CTF correction: Phase-flipped
    Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.
    Resolution: 30 A / Resolution method: FSC 0.5

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