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    Yorodumi
    - EMDB-2145: Electron microscopy of Influenza hemagglutinin (Malaysia/2506/200... -

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    Basic information

    Entry
    Database: EMDB / ID: 2145
    TitleElectron microscopy of Influenza hemagglutinin (Malaysia/2506/2004) in complex with neutralizing antibody (Fab CR8071
    KeywordsInfluenza hemagglutinin (Malaysia/2506/2004) / neutralizing antibody (Fab CR8071) / negative stained / single particle analysis
    SampleInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR8071), negative stained, single particle analysis
    SourceInfluenza B virus (B/Malaysia/2506/2004) / virus / Influenza
    Homo sapiens / human
    Map dataInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR8071), negative stained, single particle analysis
    Methodsingle particle reconstruction, at 19 A resolution
    AuthorsKhayat R / Lee JH / Dreyfus C / Laursen NS / Wilson IA / Ward AB
    CitationScience, 2012, 337, 1343-1348

    Science, 2012, 337, 1343-1348 StrPapers
    Highly conserved protective epitopes on influenza B viruses.
    Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen

    DateDeposition: Jun 26, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Aug 22, 2012 / Last update: Jun 26, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 4.8
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 4.8
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_2145.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    2.18 A/pix
    = 348.8 A
    160 pix
    2.18 A/pix
    = 348.8 A
    160 pix
    2.18 A/pix
    = 348.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.18 A
    Density
    Contour Level:4.8 (by author), 4.8 (movie #1):
    Minimum - Maximum-6.27524042 - 17.14086151
    Average (Standard dev.)0E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin-80-80-80
    Limit797979
    Spacing160160160
    CellA=B=C: 348.80002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.182.182.18
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z348.800348.800348.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-32-32-32
    NX/NY/NZ646464
    MAP C/R/S123
    start NC/NR/NS-80-80-80
    NC/NR/NS160160160
    D min/max/mean-6.27517.141-0.000

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    Supplemental data

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    Sample components

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    Entire Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibo...

    EntireName: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR8071), negative stained, single particle analysis
    Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: Trimer
    MassTheoretical: 282 kDa / Experimental: 282 kDa / Measured by: Sequence of components

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    Component #1: protein, Influenza hemagglutinin (Malaysia/2506/2004)

    ProteinName: Influenza hemagglutinin (Malaysia/2506/2004) / Oligomeric Details: Trimer / Number of Copies: 3 / Recombinant expression: Yes
    MassTheoretical: 49 kDa / Experimental: 49 kDa
    SourceSpecies: Influenza B virus (B/Malaysia/2506/2004) / virus / Influenza
    Source (engineered)Expression System: Sf9 / Vector: pDCE198
    Source (natural)Cell: Sf9

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    Component #2: protein, IgG Fab (CR8071)

    ProteinName: IgG Fab (CR8071) / Oligomeric Details: 3 monomers / Recombinant expression: Yes / Number of Copies: 3
    MassTheoretical: 45 kDa / Experimental: 45 kDa
    SourceSpecies: Homo sapiens / human

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 20 mM HEPES 8.0, 50mM NaCl / pH: 8
    Support film400 mesh gold grid with thin carbon support, glow discharged
    StainingGrids with adsorbed protein floated on Nano-W for 30 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Jan 12, 2012 / Details: Weak beam illumination
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 100000 X (nominal), 100000 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 650 - 970 nm
    Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg.
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 200 / Scanner: OTHER / Sampling size: 10.9 microns / Bit depth: 16 / OD range: 1.4 / Details: Images were collected on a CCD

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 7116
    Details: Particles were selected using DoG Picker and processed using Sparx.
    Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionAlgorithm: Cross-common lines / Software: EMAN2/Sparx / CTF correction: Each particle / Resolution: 19 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Molrep, Chimera / Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
    Details: Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
    Input PDB model: 4FQJ
    Modeling #2Software: Molrep, Chimera / Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
    Details: Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
    Input PDB model: 4FQK

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