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    Yorodumi
    - EMDB-1147: Quaternary polymorphism of replicative helicase G40P: structural ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1147
    TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
    SampleC3 architecture of Bacteriophage SPP1
    SourceBacillus phage SPP1 / virus / image: Bacillus subtilis
    Map dataBacteriophage SPP1 helicase G40P: C3 architecture
    Methodsingle particle reconstruction, at 24 A resolution
    AuthorsNunez-Ramirez R / Robledo Y / mesa P / Alonso JC
    CitationJ. Mol. Biol., 2006, 357, 1063-1076

    J. Mol. Biol., 2006, 357, 1063-1076 StrPapers
    Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
    Rafael Núñez-Ramírez / Yolanda Robledo / Pablo Mesa / Silvia Ayora / Juan Carlos Alonso / José María Carazo / Luis Enrique Donate

    DateDeposition: Aug 5, 2005 / Header (metadata) release: Aug 5, 2005 / Map release: May 17, 2006 / Last update: Aug 5, 2005

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0493
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.0493
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1147.map.gz (map file in CCP4 format, 2001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    80 pix
    4.1 A/pix
    = 328. A
    80 pix
    4.1 A/pix
    = 328. A
    80 pix
    4.1 A/pix
    = 328. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.1 A
    Density
    Contour Level:0.0243, 0.0493 (movie #1):
    Minimum - Maximum-0.157662 - 0.18685
    Average (Standard dev.)0.000114719 (0.0121095)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions808080
    Origin000
    Limit797979
    Spacing808080
    CellA=B=C: 328 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.14.14.1
    M x/y/z808080
    origin x/y/z0.0000.0000.000
    length x/y/z328.000328.000328.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-90-90-190
    NX/NY/NZ180180380
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS808080
    D min/max/mean-0.1580.1870.000

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    Supplemental data

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    Sample components

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    Entire C3 architecture of Bacteriophage SPP1

    EntireName: C3 architecture of Bacteriophage SPP1 / Oligomeric State: Homohexamer / Number of components: 1
    MassTheoretical: 300 kDa / Experimental: 300 kDa / Measured by: gel filtration chromatography

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    Component #1: protein, helicase

    ProteinName: helicase / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6
    MassTheoretical: 300 kDa / Experimental: 300 kDa
    SourceSpecies: Bacillus phage SPP1 / virus / image: Bacillus subtilis
    Strain: SPP1
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pCB506
    Source (natural)Cell: Bacteria

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.2 mg/ml
    Buffer solution: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
    pH: 7
    Support filmcollodion/carbon coated 400 mesh copper grid
    StainingGrids with adsorbed protein stained on 2% uranyl acetate for 1 minute
    VitrificationCryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2000EX
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 20 e/A2 / Illumination mode: OTHER
    LensMagnification: 60000 X (nominal) / Imaging mode: OTHER
    Specimen HolderHolder: Eucentric / Model: OTHER
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 40 / Scanner: ZEISS SCAI / Sampling size: 21 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 700 / Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionAlgorithm: Random Conical Tilt / Software: SPIDER Xmipp / Resolution: 24 A / Resolution method: FSC 0.5

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