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    - EMDB-1817: Structure of S. cerevisiae anaphase promoting complex with the co... -

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    Basic information

    Entry
    Database: EMDB / ID: 1817
    TitleStructure of S. cerevisiae anaphase promoting complex with the co-activator Cdh1
    Keywordsanaphase promoting complex / cyclosome / APC / APC/C / cell cycle / D-box / KEN-box / co-activator / Cdh1 / tetraticopeptide repeats / TPR / ubiquitylation / cyclin
    SampleStructure of S. cerevisiae anaphase promoting complex with the co-activator Cdh1
    SourceSaccharomyces cerevisiae / yeast / Baker's yeast /
    Map dataStructure of S. cerevisiae anaphase promoting complex with the co-activator Cdh1
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsdaFonseca PCA / Kong EH / Zhang Z / Schreiber A / Williams MA / Morris EP / Barford D
    CitationNature, 2011, 470, 274-278

    Nature, 2011, 470, 274-278 StrPapers
    Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
    Paula C A da Fonseca / Eric H Kong / Ziguo Zhang / Anne Schreiber / Mark A Williams / Edward P Morris / David Barford

    DateDeposition: Oct 27, 2010 / Header (metadata) release: Dec 9, 2010 / Map release: Dec 17, 2010 / Last update: Oct 27, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.15
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.15
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1817.map.gz (map file in CCP4 format, 10720 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    140 pix
    3.47 A/pix
    = 485.8 A
    140 pix
    3.47 A/pix
    = 485.8 A
    140 pix
    3.47 A/pix
    = 485.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.47 A
    Density
    Contour Level:0.15 (by emdb), 0.15 (movie #1):
    Minimum - Maximum-0.529598 - 0.881486
    Average (Standard dev.)0.00224508 (0.0370314)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions140140140
    Origin-69-70-70
    Limit706969
    Spacing140140140
    CellA=B=C: 485.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.473.473.47
    M x/y/z140140140
    origin x/y/z0.0000.0000.000
    length x/y/z485.800485.800485.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-70-69-70
    NC/NR/NS140140140
    D min/max/mean-0.5300.8810.002

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    Supplemental data

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    Sample components

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    Entire Structure of S. cerevisiae anaphase promoting complex with the co...

    EntireName: Structure of S. cerevisiae anaphase promoting complex with the co-activator Cdh1
    Number of components: 2

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    Component #1: protein, Anaphase promoting complex

    ProteinName: Anaphase promoting complex / a.k.a: Anaphase promoting complex or cyclosome / Recombinant expression: No
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /

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    Component #2: protein, Cdh1

    ProteinName: Cdh1 / a.k.a: Cdh1 / Recombinant expression: Yes
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    StainingGrids were stained using 2% w/v uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Details: Sample stained using uranyl acetate and imaged at room temperature
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Room temperature side entry / Model: OTHER
    CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionResolution: 20 A / Resolution method: FSC 0.5

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