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    Yorodumi
    - EMDB-1994: Negative stain reconstruction of the Saccharomyces cerevisiae pro... -

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    Basic information

    Entry
    Database: EMDB / ID: 1994
    TitleNegative stain reconstruction of the Saccharomyces cerevisiae proteasome lid
    Keywords26S / 19S / proteasome / yeast lid / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase
    SampleSaccharomyces cerevisiae proteasome lid subcomplex
    SourceSaccharomyces cerevisiae / yeast / Baker's Yeast /
    Map datamap of endogenous Saccharomyces cerevisiae proteasome lid
    Methodsingle particle reconstruction, at 15 A resolution
    AuthorsLander GC / Estrin E / Matyskiela M / Bashore C / Nogales E / Martin A
    CitationNature, 2012, 482, 186-191

    Nature, 2012, 482, 186-191 StrPapers
    Complete subunit architecture of the proteasome regulatory particle.
    Gabriel C Lander / Eric Estrin / Mary E Matyskiela / Charlene Bashore / Eva Nogales / Andreas Martin

    DateDeposition: Nov 18, 2011 / Header (metadata) release: Jan 6, 2012 / Map release: Jan 6, 2012 / Last update: Nov 18, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 5
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1994.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2.76 A/pix
    = 353.28 A
    128 pix
    2.76 A/pix
    = 353.28 A
    128 pix
    2.76 A/pix
    = 353.28 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.76 A
    Density
    Contour Level:5 (by author), 5 (movie #1):
    Minimum - Maximum-5.48156 - 17.3354
    Average (Standard dev.)-5.82217e-09 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-64-64-64
    Limit636363
    Spacing128128128
    CellA=B=C: 353.28 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.762.762.76
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z353.280353.280353.280
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS-64-64-64
    NC/NR/NS128128128
    D min/max/mean-5.48217.335-0.000

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    Supplemental data

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    Sample components

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    Entire Saccharomyces cerevisiae proteasome lid subcomplex

    EntireName: Saccharomyces cerevisiae proteasome lid subcomplex / Details: monodisperse / Number of components: 1 / Oligomeric State: 8 subunit complex
    MassTheoretical: 361 kDa / Experimental: 361 kDa / Measured by: Mass Spectrometry

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    Component #1: protein, lid

    ProteinName: lid / a.k.a: lid / Oligomeric Details: monomer
    Details: lid was purified from endogenous proteasome holoenzyme using a 1M salt wash
    Recombinant expression: No / Number of Copies: 1
    MassTheoretical: 361 kDa / Experimental: 361 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast /
    Strain: YYS40
    External referencesInterPro: InterPro: 002015 / Gene Ontology: GO: 0008541

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.009 mg/ml
    Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5 mM MgCl2, 0.5mM EDTA, 1mM DTT, 10% glycerol
    pH: 7.6
    Support film200 mesh Cu grid
    StainingProtein adsorbed to grid for 1 minute, then passed over four 50uL drops of 2% w/v uranyl formate, 5 seconds on each drop
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20 / Date: Apr 2, 2011 / Details: Data acquired using Leginon
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal), 80000 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
    Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1200 nm
    Specimen HolderHolder: Room temp single tilt / Model: SIDE ENTRY, EUCENTRIC / Temperature: 78 K ( 78 - 78 K)
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 250

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 33478
    Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
    Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph / Resolution: 15 A / Resolution method: FSC 0.5

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