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    - EMDB-1134: Polymorphism and double hexamer structure in the archaeal minichr... -

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    Basic information

    Entry
    Database: EMDB / ID: 1134
    TitlePolymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
    SampleArchaeal helicase MCM from Methanobacterium thermoautotrophicum
    SourceMethanothermobacter thermautotrophicus / archaea / thermophilic / Methanobacterium thermoautotrophicum
    Map datatest map
    Methodsingle particle reconstruction, at 25 A resolution
    AuthorsGomez-Llorente Y / Fletcher RJ / Chen XS / Carazo JM / San Martin C
    CitationJ. Biol. Chem., 2005, 280, 40909-40915

    J. Biol. Chem., 2005, 280, 40909-40915 StrPapers
    Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
    Yacob Gómez-Llorente / Ryan J Fletcher / Xiaojiang S Chen / José M Carazo / Carmen San Martín

    DateDeposition: Mar 16, 2005 / Header (metadata) release: Jul 1, 2005 / Map release: Jul 1, 2006 / Last update: Mar 16, 2005

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.008
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.008
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1134.map.gz (map file in CCP4 format, 3457 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    96 pix
    3.5 A/pix
    = 336. A
    96 pix
    3.5 A/pix
    = 336. A
    96 pix
    3.5 A/pix
    = 336. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.5 A
    Density
    Contour Level:0.00163, 0.008 (movie #1):
    Minimum - Maximum-0.092504 - 0.0759447
    Average (Standard dev.)-0.000648781 (0.00679169)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions969696
    Origin-48-48-48
    Limit474747
    Spacing969696
    CellA=B=C: 336 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.53.53.5
    M x/y/z969696
    origin x/y/z0.0000.0000.000
    length x/y/z336.000336.000336.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-90-90-190
    NX/NY/NZ180180380
    MAP C/R/S123
    start NC/NR/NS-48-48-48
    NC/NR/NS969696
    D min/max/mean-0.0930.076-0.001

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    Supplemental data

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    Sample components

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    Entire Archaeal helicase MCM from Methanobacterium thermoautotrophicum

    EntireName: Archaeal helicase MCM from Methanobacterium thermoautotrophicum
    Oligomeric State: homododecamer / Number of components: 1
    MassTheoretical: 900 kDa / Experimental: 900 kDa / Measured by: gel filtration

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    Component #1: protein, minichromosome maintenance protein

    ProteinName: minichromosome maintenance protein / a.k.a: MCM / Oligomeric Details: dodecamer / Recombinant expression: Yes / Number of Copies: 12
    MassTheoretical: 75.6 MDa / Experimental: 75.6 MDa
    SourceSpecies: Methanothermobacter thermautotrophicus / archaea / thermophilic / Methanobacterium thermoautotrophicum
    Strain: Delta H
    Source (engineered)Expression System: Escherichia coli / bacteria /
    External referencesInterPro: InterPro: 001208 / Gene Ontology: GO: 0006270

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml
    Buffer solution: 50 mM Tris.HCl pH 8.0, 1 mM DTT, 50 mM to 1M NaCl
    pH: 8
    Support filmglow discharged, collodion/carbon coated copper grids
    Staining2% uranyl acetate
    VitrificationCryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 1200EXII
    Details: he make and model of the microscope. Jeol 1200 EX-II. Standard Jeol 1200 holder
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 60000 X (nominal) / Astigmatism: visually corrected at 100,000x / Cs: 5.6 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: side entry / Model: OTHER
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 1200 / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionAlgorithm: projection matching / Software: SPIDER, XMIPP / Resolution: 25 A / Resolution method: 3D SSNR = 1
    Euler angles: theta between 75 and 90, phi between 0 and 360
    Details: reconstructed with ART

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    Atomic model buiding

    Modeling #1Software: Amira

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