Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1470: Molecular structure of the ParM polymer and the mechanism leading... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1470
    TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
    KeywordsGTPase / molecular switch / filament / ParM
    SampleParM filament
    SourceEscherichia coli / bacteria /
    Map dataA volume file of ParM filament
    Methodhelical reconstruction, at 23 A resolution
    AuthorsPopp D / Narita A / Oda T / Fujisawa T / Matsuo H / Nitanai Y / Iwasa M / Maeda K / Onishi H / Maeda Y
    CitationEMBO J., 2008, 27, 570-579

    EMBO J., 2008, 27, 570-579 StrPapers
    Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
    David Popp / Akihiro Narita / Toshiro Oda / Tetsuro Fujisawa / Hiroshi Matsuo / Yasushi Nitanai / Mitsusada Iwasa / Kayo Maeda / Hirofumi Onishi / Yuichiro Maéda

    DateDeposition: Feb 14, 2008 / Header (metadata) release: Feb 19, 2008 / Map release: Mar 31, 2009 / Last update: Feb 14, 2008

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 9.0672E-5
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 9.0672E-5
    • Imaged by UCSF CHIMERA
    • Download
    3D viewer /

    View / / Stereo:
    Center
    Zoom
    Scale
    slabnear <=> far

    fix: /
    Orientation
    Orientation Rotation
    misc. /
    Show/hide
    Supplemental images

    Downloads & links

    -
    Map

    Fileemd_1470.map.gz (map file in CCP4 format, 264 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    42 pix
    4.01 A/pix
    = 168.462 A
    40 pix
    4.01 A/pix
    = 160.44 A
    40 pix
    4.01 A/pix
    = 160.44 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.011 A
    Density
    Contour Level:0.00012, 9.07E-5 (movie #1):
    Minimum - Maximum-6.98964e-05 - 0.000182333
    Average (Standard dev.)6.82298e-06 (4.5134e-05)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions404042
    Origin000
    Limit393941
    Spacing404042
    CellA: 160.44 A / B: 160.44 A / C: 168.462 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.0114.0114.011
    M x/y/z404042
    origin x/y/z0.0000.0000.000
    length x/y/z160.440160.440168.462
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-55-55-55
    NX/NY/NZ111111111
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS404042
    D min/max/mean-0.0000.0000.000

    -
    Supplemental data

    -
    Sample components

    -
    Entire ParM filament

    EntireName: ParM filament / Number of components: 1 / Oligomeric State: Filament
    MassTheoretical: 35 kDa

    -
    Component #1: protein, ParM

    ProteinName: ParM / a.k.a: ParM / Oligomeric Details: Helical filament / Recombinant expression: Yes / Number of Copies: 10
    SourceSpecies: Escherichia coli / bacteria /
    Source (engineered)Expression System: Escherichia coli / bacteria /

    +
    Experimental details

    -
    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED
    Sample solutionSpecimen conc.: 0.14 mg/ml
    Buffer solution: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
    pH: 7.5
    Staining1.0 % uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

    -
    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010HC
    Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
    LensImaging mode: BRIGHT FIELD
    Specimen HolderModel: OTHER

    -
    Image acquisition

    Image acquisitionNumber of digital images: 7 / Sampling size: 7 microns

    -
    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionSoftware: EOS / CTF correction: Each filament / Resolution: 23 A / Resolution method: FSC 0.5

    -
    Atomic model buiding

    Modeling #1Software: situs / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
    Input PDB model: 1MWM
    Chain ID: 1MWM_A
    Output model

    +
    About Yorodumi

    -
    News

    -
    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    -
    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    +
    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

    +
    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

    Read more

    -
    Yorodumi

    Thousand views of thousand structures

    • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
    • All the functionalities will be ported from the levgacy version.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

    Read more