Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271

Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271

Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271

Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271
EMDB-1127: Mechanism for the disassembly of the posttermination complex infe... - Yorodumi

Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1127: Mechanism for the disassembly of the posttermination complex infe... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1127
    TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
    Sample50S.EF-G.GDPNP.RRF complex from E.coli
    SourceEscherichia coli / bacteria /
    Map dataThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
    Methodsingle particle reconstruction, at 15.5 A resolution
    AuthorsGao N / Zavialov AV / Li W / Sengupta J / Valle M / Gursky RP / Ehrenberg M / Frank J
    CitationMol. Cell, 2005, 18, 663-674

    Mol. Cell, 2005, 18, 663-674 StrPapers
    Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
    Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank

    DateDeposition: May 11, 2005 / Header (metadata) release: May 11, 2005 / Map release: May 11, 2006 / Last update: May 11, 2005

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 60
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 60
    • 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_1127.map.gz (map file in CCP4 format, 8584 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.82 A
    Density
    Contour Level:55.3, 60 (movie #1):
    Minimum - Maximum-123.87 - 336.361
    Average (Standard dev.)3.60572 (29.4095)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions130130130
    Origin-65-65-65
    Limit646464
    Spacing130130130
    CellA=B=C: 366.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.822.822.82
    M x/y/z130130130
    origin x/y/z0.0000.0000.000
    length x/y/z366.600366.600366.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-90-90-190
    NX/NY/NZ180180380
    MAP C/R/S123
    start NC/NR/NS-65-65-65
    NC/NR/NS130130130
    D min/max/mean-123.870336.3613.606

    -
    Supplemental data

    -
    Sample components

    -
    Entire 50S.EF-G.GDPNP.RRF complex from E.coli

    EntireName: 50S.EF-G.GDPNP.RRF complex from E.coli / Number of components: 3

    -
    Component #1: ribosome-prokaryote, 50S subunit

    Ribosome-prokaryoteName: 50S subunit / Prokaryote: LSU 50S / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

    -
    Component #2: protein, RRF

    ProteinName: RRF / Recombinant expression: No / Number of Copies: 1
    SourceSpecies: Escherichia coli / bacteria /

    -
    Component #3: protein, EF-G

    ProteinName: EF-G / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: polymix buffer / pH: 7.5
    Support filmQuantifoil holley carbon film grids
    StainingCryo-EM
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
    Details: Vitrification instrument: two-sided blotting plunger

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Feb 1, 2003
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 49700 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4800 nm
    Specimen HolderHolder: Cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 32171 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: defocus groups / Resolution: 15.5 A / Resolution method: FSC 0.5
    Details: Amplitude correction was applied using low-angle x-ray scattering data.

    -
    Atomic model buiding

    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