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    - EMDB-2013: Electron microscopy negative staining map of the cross-linked p97... -

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    Basic information

    Entry
    Database: EMDB / ID: 2013
    TitleElectron microscopy negative staining map of the cross-linked p97-Ufd1-Npl4 complex
    KeywordsEM / p97 / Ufd1-Npl4 / asymmetric complex / ATPase
    Samplep97-Ufd1-Npl4 cross-linked with glutaraldehyde
    SourceMus musculus / mammal / House mouse /
    Rattus norvegicus / mammal / Norway rat /
    Map dataSurface rendered p97-ATPase in complex with the adaptor Ufd1-Npl4
    Methodsingle particle reconstruction, at 28 A resolution
    AuthorsBebeacua C / Forster A / McKeown C / Meyer HH / Zhang X / Freemont PS
    CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 1098-1103

    Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 1098-1103 StrPapers
    Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy.
    Cecilia Bebeacua / Andreas Förster / Ciarán McKeown / Hemmo H Meyer / Xiaodong Zhang / Paul S Freemont

    DateDeposition: Dec 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Dec 23, 2011

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    Movie
    • Surface view with section colored by density value
    • Surface level: 4.2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 4.2
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_2013.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    3.53 A/pix
    = 451.84 A
    128 pix
    3.53 A/pix
    = 451.84 A
    128 pix
    3.53 A/pix
    = 451.84 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.53 A
    Density
    Contour Level:4.2 (by author), 4.2 (movie #1):
    Minimum - Maximum-1.68775 - 13.4836
    Average (Standard dev.)0.115421 (0.819604)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-64-64-64
    Limit636363
    Spacing128128128
    CellA=B=C: 451.84 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.533.533.53
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z451.840451.840451.840
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    MAP C/R/S123
    start NC/NR/NS-64-64-64
    NC/NR/NS128128128
    D min/max/mean-1.68813.4840.115

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    Supplemental data

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    Sample components

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    Entire p97-Ufd1-Npl4 cross-linked with glutaraldehyde

    EntireName: p97-Ufd1-Npl4 cross-linked with glutaraldehyde / Number of components: 3
    Oligomeric State: One hexamer of p97 binds to one Ufd1-Npl4 dimer
    MassTheoretical: 623 kDa / Experimental: 623 kDa

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    Component #1: protein, p97

    ProteinName: p97 / a.k.a: p97 / Number of Copies: 1 / Recombinant expression: Yes
    SourceSpecies: Mus musculus / mammal / House mouse /
    Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
    Strain: Rosetta
    Source (natural)Location in cell: Cytoplasm

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    Component #2: protein, Ufd1

    ProteinName: Ufd1 / a.k.a: Ufd1 / Recombinant expression: Yes / Number of Copies: 1
    SourceSpecies: Mus musculus / mammal / House mouse /
    Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
    Strain: Rosetta
    Source (natural)Location in cell: Cytoplasm

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    Component #3: protein, Npl4

    ProteinName: Npl4 / a.k.a: Npl4 / Number of Copies: 1 / Recombinant expression: Yes
    SourceSpecies: Rattus norvegicus / mammal / Norway rat /
    Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
    Strain: Rosetta
    Source (natural)Location in cell: Cytoplasm

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.05 mg/ml / Buffer solution: 25 mM HEPES, 500 mM KCl / pH: 8
    Support film200 mesh copper grid
    StainingGrids with adsorbed protein floated on 2% w/v uranyl acetate for 60 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jul 1, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 50000 X (nominal), 50000 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm / Energy filter: FEI
    Specimen HolderHolder: RT / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: GENERIC CCD

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    Image acquisition

    Image acquisitionNumber of digital images: 1000

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 15000 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Back Projection / Software: IMAGIC / Resolution: 28 A / Resolution method: FSC

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