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    Yorodumi
    - EMDB-1987: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3) -

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    Basic information

    Entry
    Database: EMDB / ID: 1987
    TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3)
    KeywordsStructural protein / cytoskeleton / contractile filament / motor activity / myosin binding / actin binding / ATP catabolic process / rigor state
    SampleF-actin-myo1E-tropomyosin complex (conformation 3)
    SourceOryctolagus cuniculus / mammal / Rabbit /
    Gallus gallus / bird / Chicken /
    Dictyostelium discoideum / fungus / Slime mold /
    Map dataConformation 3 of the F-actin-myo1E-tropomyosin complex
    Methodhelical reconstruction, at 7.7 A resolution
    AuthorsBehrmann E / Mueller M / Penczek PA / Mannherz HG / Manstein DJ / 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 / Header (metadata) release: Aug 1, 2012 / Map release: Aug 1, 2012 / Last update: Nov 14, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0125
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.0125
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4a7f
    • Surface level: 0.0125
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1987.map.gz (map file in CCP4 format, 22001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    220 pix
    1.84 A/pix
    = 404.8 A
    160 pix
    1.84 A/pix
    = 294.4 A
    160 pix
    1.84 A/pix
    = 294.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.84 A
    Density
    Contour Level:0.0125 (by author), 0.0125 (movie #1):
    Minimum - Maximum0E-8 - 0.07019328
    Average (Standard dev.)0.00156007 (0.00584454)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160220
    Origin000
    Limit159159219
    Spacing160160220
    CellA: 294.4 A / B: 294.4 A / C: 404.80002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.841.841.84
    M x/y/z160160220
    origin x/y/z0.0000.0000.000
    length x/y/z294.400294.400404.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS160160220
    D min/max/mean-0.0000.0700.002

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    Supplemental data

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    Sample components

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    Entire F-actin-myo1E-tropomyosin complex (conformation 3)

    EntireName: F-actin-myo1E-tropomyosin complex (conformation 3) / Details: 7 to 7 to 1 (actin to myosin to tropomyosin) / Number of components: 3 / Oligomeric State: Pentameric

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    Component #1: protein, F-actin

    ProteinName: F-actin / a.k.a: actin filament / Oligomeric Details: Filament / Number of Copies: 14 / Recombinant expression: No
    SourceSpecies: Oryctolagus cuniculus / mammal / Rabbit /
    Source (natural)Location in cell: Sarcoplasm / Organ or tissue: Skeletal muscle
    External referencesGene Ontology: GO: 0042643 / InterPro: InterPro: 004000

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    Component #2: protein, tropomyosin 1 (alpha)

    ProteinName: tropomyosin 1 (alpha) / a.k.a: tropomyosin 1 (alpha) / Oligomeric Details: Filament of dimers / Recombinant expression: Yes / Number of Copies: 2
    SourceSpecies: Gallus gallus / bird / Chicken /
    Source (engineered)Expression System: Escherichia coli (strain bl21 de3) / bacteria /
    Vector: pJC20
    Source (natural)Organ or tissue: Gizzard
    External referencesInterPro: InterPro: 000533 / Gene Ontology: GO: 0005862

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    Component #3: protein, myoE

    ProteinName: myoE / a.k.a: myosin 1E / Oligomeric Details: filament / Recombinant expression: Yes / Number of Copies: 14
    SourceSpecies: Dictyostelium discoideum / fungus / Slime mold / / Strain: AX2
    Source (engineered)Expression System: Dictyostelium discoideum / fungus / / Vector: pDXA-3H
    External referencesGene Ontology: GO: 0045160 / InterPro: InterPro: 001609

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED / Delta z: 27.6 A / Delta phi: 166.5 deg.
    Sample solutionSpecimen conc.: 0.01 mg/ml
    Buffer solution: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine
    pH: 7.2
    Support filmC-Flat CF-2/1-4C copper 400 mesh
    VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 90 % / Method: Manual blotting for approximately 15 seconds / Details: Vitrification instrument: Gatan Cryoplunge 3

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3200FSC
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal), 169644 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
    Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 750 - 1500 nm / Energy filter: in-column Omega filter / Energy window: 0-12 eV
    Specimen HolderHolder: cryogenic stage with side entry access / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 77 K
    CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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    Image acquisition

    Image acquisitionNumber of digital images: 836 / Sampling size: 15.6 microns / Bit depth: 14
    Details: Over 3000 images were taken of which only the best 836 were used for processing

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    Image processing

    ProcessingMethod: helical reconstruction / Details: Particles were selected by hand using e2helixboxer
    3D reconstructionAlgorithm: IHRSR / Software: SPARX / CTF correction: each particle / Details: Particles were classified using CODIM / Resolution: 7.7 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: DireX / Refinement protocol: flexible / Refinement space: REAL
    Details: Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera
    Input PDB model: 1LKX
    Chain ID: 1LKX_C
    Output model

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