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    Yorodumi
    - EMDB-1961: Symmetry-free cryo-EM map of TRiC-AMP-PNP -

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    Basic information

    Entry
    Database: EMDB / ID: 1961
    TitleSymmetry-free cryo-EM map of TRiC-AMP-PNP
    KeywordsTRiC/CCT / chaperonin / cryo-EM / protein folding
    Samplebovine TRiC/CCT in the AMP-PNP state
    SourceBos taurus / mammal / bovine /
    Map datasymmetry-free cryo-EM density of TRiC-AMP-PNP
    Methodsingle particle reconstruction, at 10.7 A resolution
    AuthorsCong Y / Schroder GF / Meyer AS / Jakana J / Ma B / Dougherty MT / Schmid MF / Reissmann S / Levitt M / Ludtke SL / Frydman J / Chiu W
    CitationEMBO J., 2012, 31, 720-730

    EMBO J., 2012, 31, 720-730 StrPapers
    Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
    Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu

    DateDeposition: Sep 5, 2011 / Header (metadata) release: Feb 6, 2012 / Map release: Feb 6, 2012 / Last update: Sep 5, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.13
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1.13
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4a0v
    • Surface level: 1.13
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1961.map.gz (map file in CCP4 format, 11665 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    144 pix
    2.4 A/pix
    = 345.6 A
    144 pix
    2.4 A/pix
    = 345.6 A
    144 pix
    2.4 A/pix
    = 345.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.4 A
    Density
    Contour Level:1.13 (by author), 1.13 (movie #1):
    Minimum - Maximum-0.37267885 - 2.16418886
    Average (Standard dev.)0.06878981 (0.26539356)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions144144144
    Origin-72-72-72
    Limit717171
    Spacing144144144
    CellA=B=C: 345.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.42.42.4
    M x/y/z144144144
    origin x/y/z0.0000.0000.000
    length x/y/z345.600345.600345.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS-72-72-72
    NC/NR/NS144144144
    D min/max/mean-0.3732.1640.069

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    Supplemental data

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    Sample components

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    Entire bovine TRiC/CCT in the AMP-PNP state

    EntireName: bovine TRiC/CCT in the AMP-PNP state / Number of components: 2 / Oligomeric State: 16-mer
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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    Component #1: protein, bovine TRiC

    ProteinName: bovine TRiC / a.k.a: TRiC or CCT / Oligomeric Details: 16-mer / Recombinant expression: No
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa
    SourceSpecies: Bos taurus / mammal / bovine /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1 mg/ml
    Support film200-mesh Quantifoil holey grid
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 100 % / Method: Two-side blotting for 1 second before plunging / Details: Vitrification instrument: FEI vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3200FSC
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Astigmatism: Objective lens astigmatism correction / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3000 nm / Energy filter: JEOL in-column omega energy filter / Energy window: 0-20 eV
    Specimen HolderHolder: Side entry / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 101 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 700 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 29374 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: projection matching / Software: EMAN1.8 / CTF correction: each micrograph
    Details: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps
    Resolution: 10.7 A / Resolution method: FSC 0.5

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