Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-3deg: Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 3deg
    TitleComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
    DescriptorRNA binding protein/RNA Complex
    KeywordsRIBOSOME / ribosome / translation / LepA / EF4 / GTP-binding / Membrane / Nucleotide-binding / Antibiotic resistance / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Methylation
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron microscopy (10.9 A resolution)
    AuthorsConnell, S.R. / Topf, M. / Qin, Y. / Wilson, D.N. / Mielke, T. / Fucini, P. / Nierhaus, K.H. / Spahn, C.M.T.
    CitationNat. Struct. Mol. Biol., 2008, 15, 910-915

    Nat. Struct. Mol. Biol., 2008, 15, 910-915 StrPapers
    A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
    Sean R Connell / Maya Topf / Yan Qin / Daniel N Wilson / Thorsten Mielke / Paola Fucini / Knud H Nierhaus / Christian M T Spahn

    DateDeposition: Jun 10, 2008 / Release: Aug 19, 2008 / Last modification: Apr 16, 2014

    -
    Structure visualization

    Movie
    • Deposited structure unit
    • Imaged by Jmol
    • Download
    • Simplified surface model + fitted atomic model
    • EMDB-1524
    • Imaged by Jmol
    • Download
    3D viewer /

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

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

    Downloads & links

    -
    Assembly

    Deposited unit
    A: A/L-tRNA
    B: P-tRNA
    E: 30S RNA helix 8
    F: 30S RNA helix 14
    G: 50S RNA helix 42-44
    I: 50S RNA helix 95
    J: 50S RNA helix 71
    K: 50S RNA helix 92
    C: GTP-binding protein lepA
    D: 30S ribosomal protein S12
    H: 50S ribosomal protein L11

    190 kDa, 11 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    190,06011
    Polyers190,06011
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
    Download

    -
    Components

    -
    RNA chain , 8 types, 8 molecules ABEFGIJK

    #1RNA chain / A/L-tRNA / Source: Escherichia coli (gene. exp.)
    #2RNA chain / P-tRNA / Source: Escherichia coli (gene. exp.)
    #3RNA chain / 30S RNA helix 8 / Source: Escherichia coli (gene. exp.)
    #4RNA chain / 30S RNA helix 14 / Source: Escherichia coli (gene. exp.)
    #5RNA chain / 50S RNA helix 42-44 / Source: Escherichia coli (gene. exp.)
    #6RNA chain / 50S RNA helix 95 / Source: Escherichia coli (gene. exp.)
    #7RNA chain / 50S RNA helix 71 / Source: Escherichia coli (gene. exp.)
    #8RNA chain / 50S RNA helix 92 / Source: Escherichia coli (gene. exp.)

    -
    polypeptide(L) / 30S ribosomal protein ... / 50S ribosomal protein ... , 3 types, 3 molecules CDH

    #10polypeptide(L) / 30S ribosomal protein S12 / Source: Escherichia coli (gene. exp.) / References: UniProt: P0A7S3
    #11polypeptide(L) / 50S ribosomal protein L11 / Source: Escherichia coli (gene. exp.) / References: UniProt: P0A7J7
    #9polypeptide(L) / GTP-binding protein lepA / Fragment: EF4 / Source: Escherichia coli (gene. exp.) / References: UniProt: P60785

    +
    Experimental details

    -
    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY

    -
    Electron microscopy imaging

    CameraType: KODAK SO163 FILM
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

    -
    Processing

    Image selectionSoftware name: Situs, Mod-EM, Flex-EM
    3D reconstructionResolution: 10.9 A
    Atomic model buildingSoftware name: Situs, Mod-EM, Flex-EM / Ref protocol: rigid body and flexible fitting
    Number of atoms included #LASTProtein: 6229 / Nucleic acid: 6721 / Ligand: 0 / Solvent: 0 / Total: 12950

    +
    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