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    - EMDB-1581: Structure and functional role of dynein's microtubule-binding domain -

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    Basic information

    Entry
    Database: EMDB / ID: 1581
    TitleStructure and functional role of dynein's microtubule-binding domain
    KeywordsAssembly 1 is a helical 15 protofilaments / component name / tubulin. Assembly 2 is a monomer of the SRS-MTBD construct
    SampleSynthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
    SourceMus musculus / mammal / House Mouse /
    Map dataThis is a 3-D map of the SRS-MTBD construct
    Methodhelical reconstruction, at 35 A resolution
    AuthorsCarter AP / Garbarino JE / Wilson-Kubalek EM / Shipley WE / Cho C / Milligan RA / Vale RD / Gibbons IR
    CitationScience, 2008, 322, 1691-1695

    Science, 2008, 322, 1691-1695 StrPapers
    Structure and functional role of dynein's microtubule-binding domain.
    Andrew P Carter / Joan E Garbarino / Elizabeth M Wilson-Kubalek / Wesley E Shipley / Carol Cho / Ronald A Milligan / Ronald D Vale / I R Gibbons

    DateDeposition: Nov 5, 2008 / Header (metadata) release: Nov 7, 2008 / Map release: Jun 11, 2009 / Last update: Nov 5, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 9
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 9
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1581.map.gz (map file in CCP4 format, 8229 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    103 pix
    3.5 A/pix
    = 360.5 A
    143 pix
    3.5 A/pix
    = 500.5 A
    143 pix
    3.5 A/pix
    = 500.5 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.5 A
    Density
    Contour Level:7 (by author), 9 (movie #1):
    Minimum - Maximum-30 - 52
    Average (Standard dev.)0.367653 (12.0869)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions143143103
    Origin000
    Limit142142102
    Spacing143143103
    CellA: 500.5 A / B: 500.5 A / C: 360.5 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.53.53.5
    M x/y/z143143103
    origin x/y/z0.0000.0000.000
    length x/y/z500.500500.500360.500
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-100-100-99
    NX/NY/NZ200200200
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS143143103
    D min/max/mean-30.00052.0000.368

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    Supplemental data

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    Sample components

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    Entire Synthetic construct of dynein microtubule-binding domain (85-82) ...

    EntireName: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
    Details: The SRS-MTBD-85-82 construct has a 12 heptad long stalk, only the first 3 heptad repeats were visible in this map. No density was observed for the SRS.
    Number of components: 2
    Oligomeric State: SRS-MTBD-85-82 monomers bound to 15 protofilaments helical microtubules

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    Component #1: protein, microtubule

    ProteinName: microtubule / a.k.a: microtubule / Oligomeric Details: monomer / Recombinant expression: Yes
    SourceSpecies: Mus musculus / mammal / House Mouse /
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: RIGHT HANDED
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 90 % / Method: 1.5 sec blot / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 29000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: Field Emission Gun
    Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 10 / Sampling size: 3.5 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: Fourier methods / Software: phoelix / CTF correction: each image / Resolution: 35 A / Resolution method: phase overplots

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    Atomic model buiding

    Modeling #1Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid body. The crystal structure was manually docked into the EM density using the chimera software package.
    Input PDB model: 3ERR
    Chain ID: 3ERR_A

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