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    - PDB-1m8q: Molecular Models of Averaged Rigor Crossbridges from Tomograms of... -

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    Basic information

    Entry
    Database: PDB / ID: 1m8q
    TitleMolecular Models of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle
    DescriptorChicken Skeletal muscle Myosin II
    Chicken Skeletal muscle Myosin II Regulatory Light Chain
    Chicken Skeletal muscle Myosin II Essential Light Chain
    Rabbit Skeletal muscle Actin
    KeywordsCONTRACTILE PROTEIN / Actin-myosin complex in situ in muscle
    Specimen sourceGallus gallus / bird / chicken /
    Oryctolagus cuniculus / mammal / rabbit /
    MethodElectron microscopy (70 A resolution / Tomography / Freeze substitution)
    AuthorsChen, L.F. / Winkler, H. / Reedy, M.K. / Reedy, M.C. / Taylor, K.A.
    CitationJ. Struct. Biol., 138, 92-104

    primary. J. Struct. Biol., 138, 92-104 StrPapers
    Molecular modeling of averaged rigor crossbridges from tomograms of insect flight muscle.
    Li Fan Chen / Hanspeter Winkler / Michael K Reedy / Mary C Reedy / Kenneth A Taylor

    #1. J.STRUCT.BIOL., 2001, 133, 221-232
    Real space refinement of acto-myosin structures from sectioned muscle.
    Chen, L.F. / Blanc, E. / Chapman, M.S. / Taylor, K.A.

    #2. ULTRAMICROSCOPY, 1999, 77, 141-152
    Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle
    Winkler, H. / Taylor, K.A.

    #3. J.STRUCT.BIOL., 1997, 120, 372-386
    The use of electron tomography for structural analysis of disordered protein arrays.
    Taylor, K.A. / Tang, J. / Cheng, Y. / Winkler, H.

    DateDeposition: Jul 25, 2002 / Release: Sep 10, 2002 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    A: Skeletal muscle Myosin II
    B: Skeletal muscle Myosin II Regulatory Light Chain
    C: Skeletal muscle Myosin II Essential Light Chain
    D: Skeletal muscle Myosin II
    E: Skeletal muscle Myosin II Regulatory Light Chain
    F: Skeletal muscle Myosin II Essential Light Chain
    G: Skeletal muscle Myosin II
    H: Skeletal muscle Myosin II Regulatory Light Chain
    I: Skeletal muscle Myosin II Essential Light Chain
    P: Skeletal muscle Myosin II
    Q: Skeletal muscle Myosin II Regulatory Light Chain
    R: Skeletal muscle Myosin II Essential Light Chain
    7: Skeletal muscle Actin
    8: Skeletal muscle Actin
    9: Skeletal muscle Actin
    V: Skeletal muscle Actin
    W: Skeletal muscle Actin
    X: Skeletal muscle Actin
    Y: Skeletal muscle Actin
    Z: Skeletal muscle Actin
    0: Skeletal muscle Actin
    1: Skeletal muscle Actin
    2: Skeletal muscle Actin
    3: Skeletal muscle Actin
    4: Skeletal muscle Actin
    5: Skeletal muscle Actin

    1.1 MDa, 26 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,101,09526
    Polyers1,101,09526
    Non-polymers00
    Water0

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

    #1polypeptide(L) / Skeletal muscle Myosin II / Source: Gallus gallus (gene. exp.) / References: UniProt: P13538
    #2polypeptide(L) / Skeletal muscle Myosin II Regulatory Light Chain / Source: Gallus gallus (gene. exp.) / References: UniProt: P02609
    #3polypeptide(L) / Skeletal muscle Myosin II Essential Light Chain / Source: Gallus gallus (gene. exp.) / References: UniProt: P02604
    #4polypeptide(L) / Skeletal muscle Actin / Source: Oryctolagus cuniculus (gene. exp.) / References: UniProt: P68135

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: TOMOGRAPHY / Specimen type: FREEZE SUBSTITUTION

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    Sample preparation

    Assembly of specimenName: Insect flight muscle / Aggregation state: TISSUE
    Details: Dorsal longitudinal flight muscles of the large waterbug, Lethocerus maximus were glycerinated in the dissected thorax and stored at -20 degrees C. Fixation involved sequential tannic acid-glutaraldehyde (0.2% and 2%), cold 1% OsO4 at pH 6.0, 1% uranyl acetate block staining and Araldite 506 emgedding. Thin sections were stained with a sequence of permanganate and lead. Section were ~25 nm thick.
    ComponentName: Insect flight muscle of the large water bug Lethocerus maximus
    Details: Models are built to fit the thin, actin containing filaments labeled with endogenous myosin in the rigor state
    VitrificationDetails: No vitrification. Samples were viewed at room temperature.

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    Electron microscopy imaging

    CameraType: Kodak S0163 Film
    EM image scansNumber digital images: 36
    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: RSref
    3D reconstructionMethod: Dual axis tilt series electron tomography / Resolution: 70 A / Nominal pixel size: 15.5 A/pix
    Magnification calibration: Indicated instrument magnification
    CTF correction method: none
    Details: 3-D motifs were identified in the tomogram by first producing a cross correlation map from which peak coordinates were determined from their center of gravity. We define a 3-D motif as one, entire 38.7 nm crossbridge repeat along actin. These motifs usually contain at least four myosin heads in two paired crossbridges (single chevrons) and sometimes contain as many as six myosin heads in four paired crossbridges (double chevrons). The reference for the analysis was selected to be centered between successive troponin densities which could be identified from the in-plane projection. The individual crossbridge motifs were then subjected to multivariate statistical analysis to identify clusters of motifs showing similar crossbridge structure. These clusters formed the class averages. The choice of structure to be classified was decided by the resolution and the later process of model building. Averaging was done according to the heirarchical ascendent method. The resolution in each of the class averages was 7 nm by the spectral signal to noise ratio.
    Atomic model buildingMethod: Initial models were fit by hand using "O". The fit was then refined using real space refinement.
    Software name: RSref / Ref protocol: rigid body / Ref space: REAL
    Target criteria: Best correlation coefficient and fewest poor contacts
    Number of atoms included #LASTProtein: 76872 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 76872

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