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    Yorodumi
    - EMDB-1992: The Saccharomyces cerevisiae 26S proteasome at subnanometer resolution -

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    Basic information

    Entry
    Database: EMDB / ID: 1992
    TitleThe Saccharomyces cerevisiae 26S proteasome at subnanometer resolution
    Keywords26S / 19S / proteasome / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase
    Sample26S Proteasome
    SourceSaccharomyces cerevisiae / yeast /
    Map data26 proteasome
    Methodsingle particle reconstruction, at 9 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: 3
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 3
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1992.map.gz (map file in CCP4 format, 65537 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    256 pix
    2.17 A/pix
    = 555.52 A
    256 pix
    2.17 A/pix
    = 555.52 A
    256 pix
    2.17 A/pix
    = 555.52 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.17 A
    Density
    Contour Level:3 (by author), 3 (movie #1):
    Minimum - Maximum-21.592 - 33.7328
    Average (Standard dev.)0.0686551 (1.12869)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions256256256
    Origin161616
    Limit271271271
    Spacing256256256
    CellA=B=C: 555.52 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.172.172.17
    M x/y/z256256256
    origin x/y/z0.0000.0000.000
    length x/y/z555.520555.520555.520
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS161616
    NC/NR/NS256256256
    D min/max/mean-21.59233.7330.069

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    Supplemental data

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    Sample components

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    Entire 26S Proteasome

    EntireName: 26S Proteasome / Details: monodisperse / Number of components: 1 / Oligomeric State: holoenzyme
    MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Mass Spectrometry

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    Component #1: protein, 26S Proteasome

    ProteinName: 26S Proteasome / a.k.a: 26S Proteasome / Oligomeric Details: monomer / Details: Endogenous proteasome was purified from yeast / Recombinant expression: No / Number of Copies: 1
    MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / / Strain: YYS40
    External referencesInterPro: InterPro: 001353 / Gene Ontology: GO: 0005838

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1.7 mg/ml
    Buffer solution: 20mM HEPES, 50mM NaCl, 50mM KCl, 1mM ATP, 1mM DTT, 0.05% NP40
    pH: 7.6
    Support film400-mesh C-flats, 2um holes with 2um spacing (Protochips Inc.)
    StainingC-flat grids made hydrophilic with Solarus Plasma cleaner, 4 uL of sample applied, blotted in Vitrobot for 3 seconds with offset -1, plunged into liquid ethane
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 100 % / Method: Blot 3 seconds with -2 offset / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20 / Date: Sep 11, 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: 100000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
    Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2600 nm
    Specimen HolderHolder: Side-entry cryostage / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 9153

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 93679
    Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
    Applied symmetry: C2 (2 fold cyclic)
    3D reconstructionAlgorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph
    Details: Final map filtered to local resolution using the blocfilt function in Bsoft
    Resolution: 9 A / Resolution method: FSC 0.5

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