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    Yorodumi
    - PDB-4a7h: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2) -

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    Basic information

    Entry
    Database: PDB / ID: 4a7h
    TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)
    DescriptorACTIN
    ALPHA SKELETAL MUSCLE
    TROPOMYOSIN 1-ALPHA CHAIN
    MYOSIN IE HEAVY CHAIN (E.C.3.6.4.1)
    KeywordsSTRUCTURAL PROTEIN/HYDROLASE / STRUCTURAL PROTEIN-HYDROLASE COMPLEX / STRUCTURAL PROTEIN / CYTOSKELETON / CONTRACTILE FILAMENT / MOTOR ACTIVITY / MYOSIN BINDING / ACTIN BINDING / ATP CATABOLIC PROCESS / RIGOR STATE
    Specimen sourceOryctolagus cuniculus / mammal / RABBIT /
    Dictyostelium discoideum / fungus / SLIME MOLD /
    MethodElectron microscopy (7.8 A resolution / Helical / Vitreous ice cryo EM)
    AuthorsBehrmann, E. / Mueller, M. / Penczek, P.A. / Mannherz, H.G. / Manstein, D.J. / Raunser, S.
    CitationCell, 2012, 150, 327-338

    Cell, 2012, 150, 327-338 StrPapers
    Structure of the rigor actin-tropomyosin-myosin complex.
    Elmar Behrmann / Mirco Müller / Pawel A Penczek / Hans Georg Mannherz / Dietmar J Manstein / Stefan Raunser

    DateDeposition: Nov 14, 2011 / Release: Aug 1, 2012

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    Structure visualization

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    Assembly

    Deposited unit
    A: ACTIN, ALPHA SKELETAL MUSCLE
    B: TROPOMYOSIN 1-ALPHA CHAIN
    C: MYOSIN IE HEAVY CHAIN
    D: ACTIN, ALPHA SKELETAL MUSCLE
    E: ACTIN, ALPHA SKELETAL MUSCLE
    F: ACTIN, ALPHA SKELETAL MUSCLE
    G: ACTIN, ALPHA SKELETAL MUSCLE
    H: TROPOMYOSIN 1-ALPHA CHAIN
    I: MYOSIN IE HEAVY CHAIN
    J: MYOSIN IE HEAVY CHAIN
    hetero molecules

    481 kDa, 20 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    480,95620
    Polyers478,61910
    Non-polymers2,33610
    Water0

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

    #1polypeptide(L) / ACTIN, ALPHA SKELETAL MUSCLE / F-ACTIN, ALPHA-ACTIN-1 / Source: ORYCTOLAGUS CUNICULUS (gene. exp.) / References: UniProt: P68135
    #2polypeptide(L) / TROPOMYOSIN 1-ALPHA CHAIN / Fragment: RESIDUES 98-233 / Source: ORYCTOLAGUS CUNICULUS (gene. exp.) / References: UniProt: P58772
    #3polypeptide(L) / MYOSIN IE HEAVY CHAIN / MYOE / Fragment: RESIDUES 1-697 / Mutation: YES / Source: DICTYOSTELIUM DISCOIDEUM (gene. exp.) / References: UniProt: Q03479, EC: 3.6.4.1
    #4ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM
    #5ChemComp-CA / CALCIUM ION

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE CRYO EM

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    Sample preparation

    Assembly of specimenName: F-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 2) / Aggregation state: FILAMENT / Details: CMOS IMAGE FRAMES SELECTED BY POWER SPECTRUM
    Buffer solutionName: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
    Sample preparationpH: 7.2 / Sample conc.: 0.01 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Details: BEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.7 e/A2 / Illumination mode: LOW DOSE FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 169644 X / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 4.1 mm
    Specimen holderTemperature: 77 K
    CameraType: TEMCAM-F816
    EM image scansNumber digital images: 836
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: SPARX / Number of particles: 9650
    3D reconstructionMethod: IHRSR / Resolution: 7.8 A / Nominal pixel size: 1.84 A/pix / Actual pixel size: 1.84 A/pix / CTF correction method: EACH PARTICLE
    Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1988 (DEPOSITION ID: 10379).
    Atomic model buildingMethod: GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH
    Ref protocol: EM / Ref space: REAL
    Least-squares processHighest resolution: 7.8 A
    Refine hist #LASTHighest resolution: 7.8 A
    Number of atoms included #LASTProtein: 33360 / Nucleic acid: 0 / Ligand: 140 / Solvent: 0 / Total: 33500

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