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EMDB-1157: ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA. - Yorodumi

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    - EMDB-1157: ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA. -

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    Basic information

    Entry
    Database: EMDB / ID: 1157
    TitleATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
    SampleYeast Origin Recognition complex and Cdc6p
    SourceSaccharomyces cerevisiae / yeast / baker's yeast /
    Map data3D map of the yeast (Saccharomyces cerevisiae)DNA origin recognition complex (ORC) bound with initiation factor Cdc6p.
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsSpeck C / Chen Z / Li H / Stillman B
    CitationNat. Struct. Mol. Biol., 2005, 12, 965-971

    Nat. Struct. Mol. Biol., 2005, 12, 965-971 StrPapers
    ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
    Christian Speck / Zhiqiang Chen / Huilin Li / Bruce Stillman

    DateDeposition: Sep 7, 2005 / Header (metadata) release: Sep 7, 2005 / Map release: Sep 7, 2007 / Last update: Sep 7, 2005

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.946640809
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.946640809
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1157.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    2.54 A/pix
    = 254. A
    100 pix
    2.54 A/pix
    = 254. A
    100 pix
    2.54 A/pix
    = 254. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.54 A
    Density
    Contour Level:0.359, 0.9466408 (movie #1):
    Minimum - Maximum0.00192997 - 5.82841
    Average (Standard dev.)0.101892 (0.462275)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 254 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.542.542.54
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z254.000254.000254.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-70-70-69
    NX/NY/NZ140140140
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS100100100
    D min/max/mean0.0025.8280.102

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    Supplemental data

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    Sample components

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    Entire Yeast Origin Recognition complex and Cdc6p

    EntireName: Yeast Origin Recognition complex and Cdc6p / Details: highly purified, monodisperse / Oligomeric State: hetero-heptamer / Number of components: 7
    MassTheoretical: 500 kDa / Experimental: 500 kDa / Measured by: sedimentation

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    Component #1: protein, Orc1p

    ProteinName: Orc1p / a.k.a: ORC subunit 1 / Oligomeric Details: monomer / Details: largest subunit, ATPase / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 120 kDa / Experimental: 120 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculovirus bvORC1:6
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesInterPro: InterPro: 003593 / Gene Ontology: GO: 0005664

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    Component #2: protein, Orc2p

    ProteinName: Orc2p / a.k.a: ORC subunit 2 / Oligomeric Details: monomer / Details: The second subunit / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 73 kDa / Experimental: 73 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC2:5
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005664 / InterPro: InterPro: 007220

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    Component #3: protein, Orc3p

    ProteinName: Orc3p / a.k.a: ORC subunit 3 / Oligomeric Details: monomer / Details: The third subunit / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 72 kDa / Experimental: 72 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC3:4
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005664

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    Component #4: protein, Orc4p

    ProteinName: Orc4p / a.k.a: ORC subunit 4 / Oligomeric Details: monomer / Details: The forth subunit / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 61 kDa / Experimental: 61 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC3:4
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005664

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    Component #5: protein, Orc5p

    ProteinName: Orc5p / a.k.a: ORC subunit 5 / Oligomeric Details: monomer / Details: The fifth subunit / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 53 kDa / Experimental: 53 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC2:5
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005664

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    Component #6: protein, Orc6p

    ProteinName: Orc6p / a.k.a: ORC subunit 6 / Oligomeric Details: monomer / Details: The sixth subunit / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 50 kDa / Experimental: 50 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Hi-5 cell / Vector: baculovirus bvORC1:6
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005664

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    Component #7: protein, Cdc6p

    ProteinName: Cdc6p / a.k.a: Cdc6 / Oligomeric Details: 1 / Details: initiation factor / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 56 kDa / Experimental: 56 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast /
    Source (engineered)Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli
    Vector: pGex-6P1-CDC6
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
    External referencesGene Ontology: GO: 0005656

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.02 mg/ml
    Buffer solution: 50mM HEPES-KOH, 100mM KCl, 1mM EDTA, 1mM EGTA
    pH: 7.5
    Support film300 mesh copper grid
    StainingGrids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
    VitrificationCryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 1200EX / Date: Oct 1, 2004
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: corrected at 250,000 X / Cs: 5.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm
    Specimen HolderHolder: Eucentric / Model: OTHER / Tilt Angle: 0 - 45.0 deg.
    CameraDetector: KODAK SO-163 FILM

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 50 / Number of projections: 12000 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: random conical tilt / Software: SPIDER, EMAN / CTF correction: each film / Resolution: 20 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement protocol: rigid body / Details: manual fit using program O

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