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    Yorodumi
    - PDB-3los: Atomic Model of Mm-cpn in the Closed State -

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    Basic information

    Entry
    Database: PDB / ID: 3los
    TitleAtomic Model of Mm-cpn in the Closed State
    DescriptorChaperonin
    KeywordsCHAPERONE / Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone / ATP-binding / Nucleotide-binding
    Specimen sourceMethanococcus maripaludis / archaea
    MethodElectron microscopy (4.3 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsZhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. / Frydman, J. / Chiu, W.
    CitationNature, 2010, 463, 379-383

    Nature, 2010, 463, 379-383 StrPapers
    Mechanism of folding chamber closure in a group II chaperonin.
    Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu

    DateDeposition: Feb 4, 2010 / Release: Mar 16, 2010

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    Assembly

    Deposited unit
    A: Chaperonin
    B: Chaperonin
    C: Chaperonin
    D: Chaperonin
    E: Chaperonin
    F: Chaperonin
    G: Chaperonin
    H: Chaperonin
    I: Chaperonin
    J: Chaperonin
    K: Chaperonin
    L: Chaperonin
    M: Chaperonin
    N: Chaperonin
    O: Chaperonin
    P: Chaperonin

    933 kDa, 16 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    932,65316
    Polyers932,65316
    Non-polymers00
    Water0

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

    #1polypeptide(L) / Chaperonin / Chaperonin GroEL (Thermosome, HSP60 family) / Source: Methanococcus maripaludis (gene. exp.) / References: UniProt: Q877G8

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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: Mm-cpn with 1mM ATP/AlFx / Aggregation state: PARTICLE / Composition: 16-mer / Mol wt exp: 0.96 MDa / Mol wt theo: 0.96 MDa / Number of components: 1
    ComponentName: Methanococcus maripaludis chaperonin / Type: PROTEIN
    Buffer solutionName: ATPase buffer
    Sample preparationpH: 7.5
    VitrificationInstrument: Vitrobot / Cryogen name: ETHANE / Humidity: 100 / Method: 1 blot 3 seconds

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyMicroscope model: JEM3200FSC
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 112000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Energy filter: in column omega filter / Energy window: 0-10
    Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: side-entry / Temperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: Gatan 4kX4k CCD Camera
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    EM single particle entitySymmetry type: DIHEDRAL
    3D reconstructionMethod: Projection-match / Software: EMAN / Resolution: 4.3 A / Resolution method: FSC at 0.5 cut-off / CTF correction method: Each micrograph
    Details: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
    Atomic model buildingDetails: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
    Number of atoms included #LASTProtein: 63712 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 63712

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