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    - PDB-3iyg: Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map -

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    Basic information

    Entry
    Database: PDB / ID: 3iyg
    TitleCa model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
    DescriptorT-complex protein 1 subunit theta
    T-complex protein 1 subunit gamma
    T-complex protein 1 subunit zeta
    T-complex protein 1 subunit delta
    T-complex protein 1 subunit beta
    T-complex protein 1 subunit alpha
    T-complex protein 1 subunit eta
    KeywordsCHAPERONE / TRiC/CCT / Asymmetric / Cryo-EM / subunit arrangement / ATP-binding / Chaperone / Isopeptide bond / Nucleotide-binding / Phosphoprotein / Disulfide bond
    Specimen sourceBos taurus / mammal / bovine /
    MethodElectron microscopy (4 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsCong, Y. / Baker, M.L. / Ludtke, S.J. / Frydman, J. / Chiu, W.
    CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972

    Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972 StrPapers
    4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
    Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / Steven J Ludtke / Judith Frydman / Wah Chiu

    DateDeposition: Nov 28, 2009 / Release: Mar 16, 2010 / Last modification: Apr 7, 2010

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    Assembly

    Deposited unit
    Q: T-complex protein 1 subunit theta
    G: T-complex protein 1 subunit gamma
    Z: T-complex protein 1 subunit zeta
    D: T-complex protein 1 subunit delta
    B: T-complex protein 1 subunit beta
    E: T-complex protein 1 subunit
    A: T-complex protein 1 subunit alpha
    H: T-complex protein 1 subunit eta

    452 kDa, 8 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    451,9548
    Polyers451,9548
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

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    Polypeptide(L) , 8 types, 8 molecules QGZDBEAH

    #1polypeptide(L) / T-complex protein 1 subunit theta / TCP-1-theta, CCT-theta / Source: Bos taurus (gene. exp.) / References: UniProt: Q3ZCI9
    #2polypeptide(L) / T-complex protein 1 subunit gamma / TCP-1-gamma, CCT-gamma / Source: Bos taurus (gene. exp.) / References: UniProt: Q3T0K2
    #3polypeptide(L) / T-complex protein 1 subunit zeta / TCP-1-zeta, CCT-zeta, CCT-zeta-1 / Source: Bos taurus (gene. exp.) / References: UniProt: Q3MHL7
    #4polypeptide(L) / T-complex protein 1 subunit delta / TCP-1-delta, CCT-delta / Source: Bos taurus (gene. exp.) / References: UniProt: Q2T9X2
    #5polypeptide(L) / T-complex protein 1 subunit beta / TCP-1-beta, CCT-beta / Source: Bos taurus (gene. exp.) / References: UniProt: Q3ZBH0
    #6polypeptide(L) / T-complex protein 1 subunit / Source: Bos taurus (gene. exp.)
    #7polypeptide(L) / T-complex protein 1 subunit alpha / TCP-1-alpha, CCT-alpha / Source: Bos taurus (gene. exp.) / References: UniProt: Q32L40
    #8polypeptide(L) / T-complex protein 1 subunit eta / TCP-1-eta, CCT-eta / Source: Bos taurus (gene. exp.) / References: UniProt: Q2NKZ1

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenName: bovine TRiC (also called CCT) / Aggregation state: PARTICLE / Mol wt exp: 1 MDa / Mol wt theo: 1 MDa / Number of components: 8
    ComponentName: TRiC (also called CCT) / Type: PROTEIN
    VitrificationCryogen name: ETHANE / Temp: 101 K / Humidity: 95 / Details: vitrification using ethane as cryogen / Method: two-side blotting for 1 second before plunging

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyMicroscope model: JEM3200FSC / Date: Aug-2007 to Aug-2008
    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: 1000 nm / Cs: 4.1 mm / Astigmatism: objective lens astigmatism correction / Energy filter: in-column omega energy filter / Energy window: 0-20
    Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: side entry / Temperature: 101 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: Kodak SO163 film
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: COOT, Chimera, Modeller
    3D reconstructionMethod: Projection matching / Software: EMAN / Resolution: 4 A / Resolution method: FSC at 0.5 cut-off / Number of particles: 101000 / Nominal pixel size: 1.2 A/pix / Actual pixel size: 1.2 A/pix / CTF correction method: 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 ( Details about the particle: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps )
    Atomic model buildingMethod: Local refinement, Flexible fitting / Software name: COOT, Chimera, Modeller / Ref protocol: Local refinement, Flexible fitting / Ref space: REAL
    Number of atoms included #LASTProtein: 4134 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4134

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