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    Yorodumi
    - EMDB-5268: Three-dimensional structure of Dengue virus serotype 1 complexed ... -

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    Basic information

    Entry
    Database: EMDB / ID: 5268
    TitleThree-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab
    Keywordsvirus / dengue / serotype 1 / mature virus / human antibody / neutralizing / serotype specific / Fab
    SampleDengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
    SourceDengue virus 1 / virus / Dengue 1
    Homo sapiens / human
    Map datacryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies
    Methodsingle particle (icosahedral) reconstruction, at 7 A resolution
    AuthorsTeoh EP / Kukkaro P / Teo EW / Lim A / Tan TT / Shi PY / Yip A / Schul W / Leo S / Chan SH / Smith KGC / Ooi EE / Kemeny DM / Ng G / Ng ML / Alonso S / Fisher D / Hanson B / Lok SM / MacAry PA
    CitationSci Transl Med, 2012, 4, 139ra83-139ra83

    Sci Transl Med, 2012, 4, 139ra83-139ra83 StrPapers
    The structural basis for serotype-specific neutralization of dengue virus by a human antibody.
    Ee Ping Teoh / Petra Kukkaro / En Wei Teo / Angeline P C Lim / Tze Tong Tan / Andy Yip / Wouter Schul / Myint Aung / Victor A Kostyuchenko / Yee Sin Leo / Soh Ha Chan / Kenneth G C Smith / Annie Hoi Yi Chan / Gang Zou / Eng Eong Ooi / D Michael Kemeny / Grace K Tan / Jowin K W Ng / Mah Lee Ng / Sylvie Alonso / Dale Fisher / Pei-Yong Shi / Brendon J Hanson / Shee-Mei Lok / Paul A MacAry

    DateDeposition: Mar 15, 2011 / Header (metadata) release: Mar 23, 2011 / Map release: Jun 27, 2012 / Last update: Mar 15, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3j05
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4cau
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5268.map.gz (map file in CCP4 format, 488283 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    500 pix
    1.9 A/pix
    = 950. A
    500 pix
    1.9 A/pix
    = 950. A
    500 pix
    1.9 A/pix
    = 950. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.9 A
    Density
    Contour Level:2.5 (by author), 2.5 (movie #1):
    Minimum - Maximum-12.80239964 - 18.50806618
    Average (Standard dev.)0E-8 (0.99999994)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions500500500
    Origin-250-250-250
    Limit249249249
    Spacing500500500
    CellA=B=C: 950 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.91.91.9
    M x/y/z500500500
    origin x/y/z0.0000.0000.000
    length x/y/z950.000950.000950.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-250-250-250
    NC/NR/NS500500500
    D min/max/mean-12.80218.508-0.000

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    Supplemental data

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    Sample components

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    Entire Dengue virus serotype 1 with Fab fragment of human monoclonal ant...

    EntireName: Dengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
    Number of components: 2
    Oligomeric State: 120 Fab molecules bind to one dengue virion

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    Component #1: virus, Dengue virus 1

    VirusName: Dengue virus 1 / a.k.a: Dengue 1 / Class: VIRION / Details: strain PVP 159 / Enveloped: Yes / Empty: No / Isolate: STRAIN
    SpeciesSpecies: Dengue virus 1 / virus / Dengue 1
    Source (natural)Host Species: Aedes albopictus / arthropod / image: Aedes aegypti
    Host category: INVERTEBRATES

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    Component #2: protein, antibody Fab fragment

    ProteinName: antibody Fab fragment / a.k.a: Fab / Oligomeric Details: monomer / Recombinant expression: Yes
    MassExperimental: 50 MDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Homo sapiens / human / Vector: pTT5
    Source (natural)Location in cell: secreted / Cell: CD22plus B cells / Organ or tissue: blood

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 120 mM NaCl, 12 mM Tris-HCl, pH 8.0, 1mM EDTA
    pH: 8
    Support filmlacey carbon copper grid
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 second blotting / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TITAN KRIOS / Date: Sep 27, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 16 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 47000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 760 - 4900 nm
    Specimen HolderModel: OTHER / Temperature: 100 K
    CameraDetector: GENERIC GATAN

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    Image acquisition

    Image acquisitionNumber of digital images: 341 / Sampling size: 15 microns / Bit depth: 16 / Details: 4k x 4k Gatan CCD

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Details: The particles were selected manually. / Number of projections: 2129 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Cross-common lines / Software: EMAN, MPSA / CTF correction: Each particle / Resolution: 7 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
    Details: Protocol: rigid body. The domains were fitted separately using Fit In Map feature in Chimera
    Input PDB model: 3G7T
    Output model

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