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    - EMDB-5172: 3.6 Angstrom cryoEM structure of human adenovirus type 5 -

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    Basic information

    Entry
    Database: EMDB / ID: 5172
    Title3.6 Angstrom cryoEM structure of human adenovirus type 5
    Keywordshuman adenovirus / cryoEM / 3D reconstruction / full-atom model / interaction network
    Samplehuman adenovirus type 5
    SourceHuman adenovirus 5 / virus / human adenovirus type 5
    Map dataThe cryoEM density map is for a huge virus (920A in diameter)and the size is 2.4GB.
    Methodsingle particle (icosahedral) reconstruction, at 3.6 A resolution
    AuthorsLiu H / Jin L / Koh SBS / Atanasov I / Schein S / Wu L / Zhou ZH
    CitationScience, 2010, 329, 1038-1043

    Science, 2010, 329, 1038-1043 StrPapers
    Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.
    Hongrong Liu / Lei Jin / Sok Boon S Koh / Ivo Atanasov / Stan Schein / Lily Wu / Z Hong Zhou

    DateDeposition: Mar 9, 2010 / Header (metadata) release: May 21, 2010 / Map release: Sep 1, 2010 / Last update: Mar 9, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 8
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 8
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3iyn
    • Surface level: 8
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3izo
    • Surface level: 8
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5172.map.gz (map file in CCP4 format, 1242298 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    430 pix
    1.1 A/pix
    = 473. A
    860 pix
    1.1 A/pix
    = 946. A
    860 pix
    1.1 A/pix
    = 946. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.1 A
    Density
    Contour Level:8 (by author), 8 (movie #1):
    Minimum - Maximum-37.9406 - 48.2722
    Average (Standard dev.)0.132958 (3.9127)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions860860430
    Origin-430-4300
    Limit429429429
    Spacing860860430
    CellA: 946 A / B: 946 A / C: 473 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.11.11.1
    M x/y/z860860430
    origin x/y/z0.0000.0000.000
    length x/y/z946.000946.000473.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-430-4300
    NC/NR/NS860860430
    D min/max/mean-37.94148.2720.133

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    Supplemental data

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    Sample components

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    Entire human adenovirus type 5

    EntireName: human adenovirus type 5
    Details: E1B gene-attenuated oncolytic human adenovirus type 5 was propagated in HEK 293 cells, harvested and liberated by 3 cycles of freezing-thawing and purified by CsCl step gradient ultra-centrifugation. The virion particles were then dialyzed and resuspended in 10 mM Tris (pH 7.5), 1 mM MgCl2.
    Number of components: 15 / Oligomeric State: Icosahedral particle

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    Component #1: virus, Human adenovirus 5

    VirusName: Human adenovirus 5 / a.k.a: human adenovirus type 5 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
    MassTheoretical: 150 MDa / Experimental: 150 MDa
    SpeciesSpecies: Human adenovirus 5 / virus / human adenovirus type 5
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 10mM Tris-HCL,1mM MgCl2 / pH: 7.5
    Support film200 mesh holey carbon grid
    StainingThe virus particles were not stained.
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging
    Details: Vitrification instrument: FEI Vitrobot. Vitrification carried out in a chamber with controlled humidity.

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    Electron microscopy imaging

    ImagingMicroscope: FEI TITAN KRIOS / Date: May 1, 2009 / Details: low-dose
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensMagnification: 59000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
    Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 90 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 756 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction
    Details: 756 micrographs that clearly showed signals up to 4 Angstrom in their power spectra were selected. Individual particle images (1024 pixel by 1024 pixel) were first boxed out automatically by the autoBox program in the IMIRS package, followed by manual screening with the EMAN boxer program to keep only the well-separated, contamination-free and intact 45000 particles. The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. Determination of particle orientation and centre, and subsequent 3D reconstruction were done with the IMIRS package, enhanced by icosahedral symmetry-adapted functions.
    Number of projections: 31815 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: common lines / Software: IMIRS / CTF correction: Each particle
    Details: The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. We determined particle orientation, centre parameters and subsequent 3D reconstruction with the IMIRS package, enhanced by icosahedral symmetry-adapted functions for 3D reconstruction. We incorporated astigmatism in the CTF correction in both orientation-centre refinement and 3D reconstruction steps. The IMIRS procedure was optimized, and the data processing was completed within two months by three personal computers, each with eight 2.33GHz CPUs and 16G memory.
    Resolution: 3.6 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Output model

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