Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-2136: Negative stain EM composite structure (part 1) of the type IV sec... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 2136
    TitleNegative stain EM composite structure (part 1) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10
    SampleTraB/TraN/TraO/TraF complex encoded by pKM101
    SourceEscherichia coli / bacteria /
    Map dataCore complex part of the VirB4-core complex composite reconstruction
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsWilliams R / Wallden K / Yan J / Lian PW / Wang L / Thalassinos K / Orlova EV / Waksman G
    CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 11348-11353

    Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 11348-11353 StrPapers
    Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
    Karin Walldén / Robert Williams / Jun Yan / Pei W Lian / Luchun Wang / Konstantinos Thalassinos / Elena V Orlova / Gabriel Waksman

    DateDeposition: Jun 12, 2012 / Header (metadata) release: Jul 25, 2012 / Map release: Aug 1, 2012 / Last update: Jun 12, 2012

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.25
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 0.25
    • 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_2136.map.gz (map file in CCP4 format, 61037 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    250 pix
    1.67 A/pix
    = 417.5 A
    250 pix
    1.67 A/pix
    = 417.5 A
    250 pix
    1.67 A/pix
    = 417.5 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.67 A
    Density
    Contour Level:0.35 (by emdb), 0.25 (movie #1):
    Minimum - Maximum-1.48925638 - 1.98086631
    Average (Standard dev.)0.0111697 (0.09054922)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions250250250
    Origin-125-125-125
    Limit124124124
    Spacing250250250
    CellA=B=C: 417.5 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.671.671.67
    M x/y/z250250250
    origin x/y/z0.0000.0000.000
    length x/y/z417.500417.500417.500
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-32-32-32
    NX/NY/NZ646464
    MAP C/R/S123
    start NC/NR/NS-125-125-125
    NC/NR/NS250250250
    D min/max/mean-1.4891.9810.011

    -
    Supplemental data

    -
    Sample components

    -
    Entire TraB/TraN/TraO/TraF complex encoded by pKM101

    EntireName: TraB/TraN/TraO/TraF complex encoded by pKM101 / Number of components: 4
    Oligomeric State: 14-mer of core complex (TraN/TraO/TraF) and monomer of TraB
    MassTheoretical: 1.15 MDa / Experimental: 1.15 MDa

    -
    Component #1: protein, TraB

    ProteinName: TraB / a.k.a: VirB4
    Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
    Number of Copies: 1 / Recombinant expression: Yes
    SourceSpecies: Escherichia coli / bacteria / / Strain: pKM101 plasmid
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK IBA3C
    Source (natural)Location in cell: cell envelope

    -
    Component #2: protein, TraN

    ProteinName: TraN / a.k.a: VirB7
    Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
    Recombinant expression: Yes / Number of Copies: 14
    SourceSpecies: Escherichia coli / bacteria / / Strain: pKM101 plasmid
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK IBA3C
    Source (natural)Location in cell: cell envelope

    -
    Component #3: protein, TraO

    ProteinName: TraO / a.k.a: VirB9
    Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
    Number of Copies: 14 / Recombinant expression: Yes
    SourceSpecies: Escherichia coli / bacteria / / Strain: pKM101 plasmid
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK IBA3C
    Source (natural)Location in cell: cell envelope

    -
    Component #4: protein, TraF

    ProteinName: TraF / a.k.a: VirB10
    Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
    Recombinant expression: Yes / Number of Copies: 14
    SourceSpecies: Escherichia coli / bacteria / / Strain: pKM101 plasmid
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pASK IBA3C
    Source (natural)Location in cell: cell envelope

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Support filmGlow-discharged continuous carbon
    StainingNanoW
    VitrificationInstrument: NONE / Cryogen name: NONE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Dec 22, 2009
    Electron gunElectron source: OTHER / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
    LensMagnification: 42000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2000 nm
    Specimen HolderModel: SIDE ENTRY, EUCENTRIC
    CameraDetector: GENERIC FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 12 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 330 / Number of projections: 10000 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Common lines / Software: IMAGIC
    Details: This map is part of a composite structure of two maps.
    Resolution: 20 A / Resolution method: FSC 0.5

    +
    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