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    Yorodumi
    - PDB-4a0v: model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP -

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    Basic information

    Entry
    Database: PDB / ID: 4a0v
    Titlemodel refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
    DescriptorT-COMPLEX PROTEIN 1 SUBUNIT BETA
    KeywordsCHAPERONE / CHAPERONIN / PROTEIN FOLDING
    Specimen sourceBos taurus / mammal / CATTLE /
    MethodElectron microscopy (10.7 A resolution / Single particle / Vitreous ice)
    AuthorsCong, Y. / Schroder, G.F. / Meyer, A.S. / Jakana, J. / Ma, B. / Dougherty, M.T. / Schmid, M.F. / Reissmann, S. / Levitt, M. / Ludtke, S.L. / 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 13, 2011 / Release: Feb 15, 2012 / Last modification: Aug 12, 2015

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    Assembly

    Deposited unit
    A: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    B: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    C: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    D: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    E: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    F: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    G: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    H: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    I: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    J: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    K: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    L: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    M: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    N: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    O: T-COMPLEX PROTEIN 1 SUBUNIT BETA
    P: T-COMPLEX PROTEIN 1 SUBUNIT BETA

    882 kDa, 16 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    881,72516
    Polyers881,72516
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by software (PISA) / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / T-COMPLEX PROTEIN 1 SUBUNIT BETA / TCP-1-BETA, CCT-BETA, BOVINE TRIC / Source: BOS TAURUS (gene. exp.) / References: UniProt: Q3ZBH0

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

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    Sample preparation

    Assembly of specimenName: BOVINE TRIC IN THE AMP- PNP STATE / Aggregation state: PARTICLE
    Specimen supportDetails: HOLEY CARBON

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 4.1 mm
    Specimen holderTemperature: 101 K
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 700
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EMAN1.8 / Number of particles: 29374
    EM single particle entitySymmetry type: MIXED SYMMETRY
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.7 A / Nominal pixel size: 2.4 A/pix / Actual pixel size: 2.4 A/pix / CTF correction method: EACH MICROGRAPH
    Details: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1961. (DEPOSITION ID: 10236).
    Least-squares processHighest resolution: 10.7 A
    Refine hist #LASTHighest resolution: 10.7 A
    Number of atoms included #LASTProtein: 59707 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 59707

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