Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1499: Structure of the E. coli trigger factor bound to a translating ri... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1499
    TitleStructure of the E. coli trigger factor bound to a translating ribosome
    Keywordstrigger factor / ribosome-nascent chain complex / translating ribosome / co-translational protein folding / chaperone
    SampleEscherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
    SourceEscherichia coli / bacteria /
    Map dataStructure of the E. coli trigger factor bound to a translating ribosome
    Methodsingle particle reconstruction, at 19 A resolution
    AuthorsMerz F / Boehringer D / Schaffitzel C / Preissler S / Hoffmann A / Maier T / Rutkowska A / Lozza J / Ban N / Bukau B / Deuerling E
    CitationEMBO J., 2008, 27, 1622-1632

    EMBO J., 2008, 27, 1622-1632 StrPapers
    Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
    Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling

    DateDeposition: Apr 4, 2008 / Header (metadata) release: Apr 4, 2008 / Map release: May 29, 2009 / Last update: Apr 4, 2008

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 200
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 200
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-2vrh
    • Surface level: 200
    • 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_1499.map.gz (map file in CCP4 format, 3457 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    96 pix
    4.23 A/pix
    = 406.4 A
    96 pix
    4.23 A/pix
    = 406.4 A
    96 pix
    4.23 A/pix
    = 406.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.23333 A
    Density
    Contour Level:30 (by author), 200 (movie #1):
    Minimum - Maximum-3064.79 - 4637.19
    Average (Standard dev.)-67.8371 (417.042)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions969696
    Origin494949
    Limit144144144
    Spacing969696
    CellA=B=C: 406.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.23333333333334.23333333333334.2333333333333
    M x/y/z969696
    origin x/y/z0.0000.0000.000
    length x/y/z406.400406.400406.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ494949
    NX/NY/NZ969696
    MAP C/R/S213
    start NC/NR/NS494949
    NC/NR/NS969696
    D min/max/mean-3064.7944637.192-67.837

    -
    Supplemental data

    -
    Sample components

    -
    Entire Escherichia coli Trigger Factor associated with an Escherichia co...

    EntireName: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
    Details: monodisperse sample / Number of components: 2
    MassExperimental: 2.6 MDa

    -
    Component #1: ribosome-prokaryote, ribosome-nascent chain complex

    Ribosome-prokaryoteName: ribosome-nascent chain complex / a.k.a: translating ribosome / Details: SecM-stalled E. coli ribosome complex / Prokaryote: ALL / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

    -
    Component #2: protein, trigger factor

    ProteinName: trigger factor / a.k.a: trigger factor / Oligomeric Details: monomer
    Details: trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli
    Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria / / Strain: mutant TFS61c

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol
    pH: 7.5
    VitrificationInstrument: NONE / Cryogen name: ETHANE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: 88 K
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionScanner: OTHER / Sampling size: 6.35 microns / Details: rotating-drum scanner

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: angular reconstitution / Software: IMAGIC-5, SPIDER / CTF correction: each image
    Details: Final rounds of refinement were done using the Spider software
    Resolution: 19 A / Resolution method: FSC 0.5

    -
    Atomic model buiding

    Modeling #1Refinement protocol: rigid body / Target criteria: Cross Correlation / Refinement space: REAL / Details: Protocol: Rigid Body. exhaustive search
    Input PDB model: 1W26
    Chain ID: A
    Modeling #2Software: MOLREP / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
    Input PDB model: 2AW4
    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