Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1617: C12 symmetrised 3D reconstruction of the Shigella flexneri T3SS n... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1617
    TitleC12 symmetrised 3D reconstruction of the Shigella flexneri T3SS needle complex from negatively stained sample electron micrographs
    KeywordsShigella flexneri Type III secretion system Needle complex Microbial pathogenesis
    SampleShigella flexneri T3SS needle complex
    SourceShigella flexneri / bacteria / Dysentery bacillus
    Map dataThis is a 3D reconstruction of the Shigella flexneri 'needle complex' from negative stain images, done with C12 symmetry imposed. The resolution is 21-25A.
    Methodsingle particle reconstruction, at 25 A resolution
    AuthorsHodgkinson JL / Horsley A / Stabat D / Simon M / Johnson S / da Fonseca PCA / Morris EP / Wall JS / Lea SM / Blocker AJ
    CitationNat. Struct. Mol. Biol., 2009, 16, 477-485

    Nat. Struct. Mol. Biol., 2009, 16, 477-485 StrPapers
    Three-dimensional reconstruction of the Shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout.
    Julie L Hodgkinson / Ashley Horsley / David Stabat / Martha Simon / Steven Johnson / Paula C A da Fonseca / Edward P Morris / Joseph S Wall / Susan M Lea / Ariel J Blocker

    DateDeposition: May 1, 2009 / Header (metadata) release: May 20, 2009 / Map release: May 27, 2009 / Last update: May 1, 2009

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 1.2
    • 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_1617.map.gz (map file in CCP4 format, 23551 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    182 pix
    2.62 A/pix
    = 476.84 A
    182 pix
    2.62 A/pix
    = 476.84 A
    182 pix
    2.62 A/pix
    = 476.84 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.62 A
    Density
    Contour Level:1 (by author), 1.2 (movie #1):
    Minimum - Maximum-13.1014 - 9.57075
    Average (Standard dev.)-1.06342e-09 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions182182182
    Origin-91-91-91
    Limit909090
    Spacing182182182
    CellA=B=C: 476.84 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.622.622.62
    M x/y/z182182182
    origin x/y/z0.0000.0000.000
    length x/y/z476.840476.840476.840
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-17-17-200
    NX/NY/NZ123123401
    MAP C/R/S123
    start NC/NR/NS-91-91-91
    NC/NR/NS182182182
    D min/max/mean-13.1019.571-0.000

    -
    Supplemental data

    -
    Sample components

    +
    Entire Shigella flexneri T3SS needle complex

    EntireName: Shigella flexneri T3SS needle complex
    Details: Affinity purified using His6 tag on MxiG N-term Contains detergent (see Zenk et al., 2007)
    Number of components: 8
    Oligomeric State: Large macromolecular complex (total list of components not yet known)
    MassExperimental: 3.6 MDa / Measured by: STEM analysis

    +
    Component #1: protein, Spa24

    ProteinName: Spa24 / a.k.a: Spa24 / Oligomeric Details: Unknown
    Details: This is the MW of the monomer, which must be cleaved in its cytoplasmic portion during T3SS biogenesis.
    Recombinant expression: No
    MassTheoretical: 240 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: inner membrane protein / Cell: Gram-negative bacterium
    External referencesInterPro: InterPro: 005773 / Gene Ontology: GO: 0009306

    +
    Component #2: protein, Spa40

    ProteinName: Spa40 / a.k.a: Spa40 / Oligomeric Details: Unknown
    Details: This is the MW of the monomer, which must be cleaved in its cytoplasmic portion during T3SS biogenesis.
    Recombinant expression: No
    MassTheoretical: 400 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: polytopic-inner membrane protein / Cell: Gram-negative bacterium
    External referencesGene Ontology: GO: 0009306 / InterPro: InterPro: 006307

    +
    Component #3: protein, MxiM

    ProteinName: MxiM / a.k.a: MxiM / Details: This is the MW of the monomer. / Recombinant expression: No / Number of Copies: 12
    MassTheoretical: 150 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: outside face of outer membrane / Cell: Gram-negative bacterium
    External referencesGene Ontology: GO: 0009279

    +
    Component #4: protein, MxiI

    ProteinName: MxiI / a.k.a: MxiI / Oligomeric Details: Helical polymer / Details: This is the MW of the monomer. / Number of Copies: 10 / Recombinant expression: No
    MassTheoretical: 100 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: periplasmic space / Cell: Gram-negative bacterium
    External referencesGene Ontology: GO: 0015031

    +
    Component #5: protein, MxiG

    ProteinName: MxiG / a.k.a: MxiG / Oligomeric Details: Probable homo-24mer / Details: This is the MW of the monomer. / Number of Copies: 24 / Recombinant expression: No
    MassTheoretical: 430 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: spans inner membrane / Cell: Gram-negative bacterium
    External referencesGene Ontology: GO: 0009405

    +
    Component #6: protein, MxiJ

    ProteinName: MxiJ / a.k.a: MxiJ / Oligomeric Details: Probable homo-dodecamer
    Details: This is the MW of the monomer with its N-terminal lipid modification site processed (but MW of lipid moiety unknown).
    Recombinant expression: No / Number of Copies: 12
    MassTheoretical: 250 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: mostly periplasmic face of inner membrane / Cell: Gram-negative bacterium
    External referencesGene Ontology: GO: 0009306 / InterPro: InterPro: 006182

    +
    Component #7: protein, MxiH

    ProteinName: MxiH / a.k.a: MxiH / Oligomeric Details: helical polymer / Details: This is the MW of the monomer. / Recombinant expression: No / Number of Copies: 120
    MassTheoretical: 90 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: Extracellular / Cell: Gram-negative bacterium
    External referencesInterPro: InterPro: 011841 / Gene Ontology: GO: 0009405

    +
    Component #8: protein, MxiD

    ProteinName: MxiD / a.k.a: MxiD / Oligomeric Details: homo-dodecamer
    Details: This is the MW of the monomer without it's signal sequence included
    Recombinant expression: No / Number of Copies: 12
    MassTheoretical: 620 kDa
    SourceSpecies: Shigella flexneri / bacteria / Dysentery bacillus / Strain: Shigella flexneri M90T
    Source (natural)Organelle: Type III secretion system / Location in cell: Outer membrane / Cell: Gram-negative bacterium
    External referencesInterPro: InterPro: 003522 / Gene Ontology: GO: 0009306

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.05 mg/ml
    Buffer solution: 10mM Tris pH 8, 0.1% Triton X-100 and 1mM EDTA buffer
    pH: 8
    Support film400 mesh copper grids (Athene) covered with holey carbon film over which thin plain carbon was laid were used
    Stainingnegatively stained in unbuffered 2% aqueous uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG / Details: Low-dose mode was used
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 50000 X (nominal), 48600 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 900 nm
    Specimen HolderHolder: eucentric / Model: OTHER
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 126 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / OD range: 1

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 4 / Number of projections: 41
    Details: Numbers of particles given are for final reconstruction. We started with over 3000. Particles were selected using Ximdisp software, cut out to an initial box size of 400 by 400 pixel and coarsened to 2.62A per pixel using Label prior to further processing.
    Applied symmetry: C12 (12 fold cyclic)
    3D reconstructionAlgorithm: weighted back projection / Euler angles: Imagic beta 87-93 degrees gamma 0-30 degrees / Software: SPIDER IMAGIC5
    Details: Maps were generated from 41 individual images (selected through image processing out of an initial pool of 3000)
    Resolution: 25 A / Resolution method: FSC at 3-sigma and 0.5 cut-offs

    +
    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