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    - EMDB-1970: Negative stained image reconstruction of HIV spike protein in com... -

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    Basic information

    Entry
    Database: EMDB / ID: 1970
    TitleNegative stained image reconstruction of HIV spike protein in complex with PGT128 Fab at 14 Angstrom resolution
    KeywordsHIV / broadly neutralizing antibody / glycan shield
    SampleHIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody
    SourceHuman immunodeficiency virus / virus / Spike protien
    Homo sapiens / human
    Map dataHIV Envelope protein in complex with Fab PGT128
    Methodsingle particle reconstruction, at 14 A resolution
    AuthorsKhayat R / Pejchal R / Julien J-P / Wilson IA
    CitationScience, 2011, 334, 1097-1103

    Science, 2011, 334, 1097-1103 StrPapers
    A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.
    Robert Pejchal / Katie J Doores / Laura M Walker / Reza Khayat / Po-Ssu Huang / Sheng-Kai Wang / Robyn L Stanfield / Jean-Philippe Julien / Alejandra Ramos / Max Crispin / Rafael Depetris / Umesh Katpally / Andre Marozsan / Albert Cupo / Sebastien Maloveste / Yan Liu / Ryan McBride / Yukishige Ito / Rogier W Sanders / Cassandra Ogohara / James C Paulson / Ten Feizi / Christopher N Scanlan / Chi-Huey Wong / John P Moore / William C Olson / Andrew B Ward / Pascal Poignard / William R Schief / Dennis R Burton / Ian A Wilson

    DateDeposition: Sep 25, 2011 / Header (metadata) release: Oct 20, 2011 / Map release: Oct 21, 2011 / Last update: Sep 25, 2011

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    Structure visualization

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    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1970.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:1 (by author), 1 (movie #1):
    Minimum - Maximum-1.63715 - 3.57025
    Average (Standard dev.)0.0105322 (0.257004)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin000
    Limit159159159
    Spacing160160160
    CellA=B=C: 348.8 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-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS160160160
    D min/max/mean-1.6373.5700.011

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    Supplemental data

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    Sample components

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    Entire HIV spike protein 664G construct in complex with Fab fragment of ...

    EntireName: HIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody
    Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: One trimer binds to three Fabs
    MassExperimental: 445 kDa
    Measured by: Size exclusion chromatography and light scattering

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    Component #1: protein, Human immunodeficiency virus envelope protein

    ProteinName: Human immunodeficiency virus envelope protein / a.k.a: Spike protein / Oligomeric Details: Trimer
    Details: The PGT128 Fab was complexed to the spike protein, partially deglycosylated, purified using size exclusion chromatography, and concentrated.
    Number of Copies: 3 / Recombinant expression: Yes
    SourceSpecies: Human immunodeficiency virus / virus / Spike protien
    Strain: KNH1144 SOSIP 664G
    Source (engineered)Expression System: 293s / Vector: pP14

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    Component #2: protein, PGT128 monoclonal antibody fragment

    ProteinName: PGT128 monoclonal antibody fragment / a.k.a: Fab fragment / Oligomeric Details: Monomer / Recombinant expression: No
    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 pH 7.5, 50 mM NaCl / pH: 7.5
    Support film400 mesh copper grid
    Staining2% Uranyl Formate for 30 seconds
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Aug 11, 2011
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16 e/A2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM
    LensMagnification: 100000 X (nominal)
    Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 400 - 950 nm
    Specimen HolderHolder: eucentric / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg. / Temperature: 293 K ( 293 - 293 K)
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 357 / Sampling size: 0.109 microns / Bit depth: 16 / Details: Data collected on CCD

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 62 / Number of projections: 12824
    Details: The particles were selected using an DoG Picker, and cleaned using reference free class averaging.
    Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionAlgorithm: Cros-common lines / Euler angles: SPIDER:theta 90 degrees, phi 120 degrees / Software: Sparx / CTF correction: Micrograph and each particle / Resolution: 14 A / Resolution method: FSC 0.5

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