Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2akh: Normal mode-based flexible fitted coordinates of a non-translocat... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 2akh
    TitleNormal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli
    DescriptorProtein-export membrane protein secG
    Preprotein translocase secY subunit
    Preprotein translocase secE subunit
    KeywordsPROTEIN TRANSPORT / Protein transport / Translocation / Transmembrane / Transport
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron microscopy (14.9 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsMitra, K.M. / Schaffitzel, C. / Shaikh, T. / Tama, F. / Jenni, S. / Brooks III, C.L. / Ban, N. / Frank, J.
    CitationNature, 2005, 438, 318-324

    Nature, 2005, 438, 318-324 StrPapers
    Structure of the E. coli protein-conducting channel bound to a translating ribosome.
    Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank

    DateDeposition: Aug 3, 2005 / Release: Nov 15, 2005 / Last modification: Feb 24, 2009

    -
    Structure visualization

    Movie
    • Deposited structure unit
    • Imaged by Jmol
    • Download
    • Simplified surface model + fitted atomic model
    • EMDB-1143
    • 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
    X: Protein-export membrane protein secG
    Y: Preprotein translocase secY subunit
    Z: Preprotein translocase secE subunit
    A: Protein-export membrane protein secG
    B: Preprotein translocase secY subunit
    C: Preprotein translocase secE subunit

    128 kDa, 6 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    127,9276
    Polyers127,9276
    Non-polymers00
    Water0

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

    -
    Components

    #1polypeptide(L) / Protein-export membrane protein secG / Preprotein translocase band 1 subunit, P12 / Source: Escherichia coli (gene. exp.) / References: UniProt: P33582
    #2polypeptide(L) / Preprotein translocase secY subunit / Fragment: plug TMH 2a deleted / Mutation: DEL(40-75) / Source: Escherichia coli (gene. exp.) / References: UniProt: P03844
    #3polypeptide(L) / Preprotein translocase secE subunit / Source: Escherichia coli (gene. exp.) / References: UniProt: P16920

    +
    Experimental details

    -
    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

    -
    Sample preparation

    Assembly of specimenName: protein-conducting channel / Aggregation state: PARTICLE
    Component

    Assembly id: 1 / Details: dimer of SecYEG heterotrimer / Go id: 0015450 / Name: protein translocase activity

    IDIpr id
    1IPR004692
    2IPR002208
    3IPR005807
    VitrificationInstrument: two sided blotting plunger / Cryogen name: ETHANE / Temp: 93 K / Humidity: 90 / Method: Blot for 2 seconds before plunging

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F30 / Date: Mar 9, 2004
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 11 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 4300 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm
    Specimen holderSpecimen holder model: OTHER / Specimen holder type: Cryo Stage / Temperature: 93 K
    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: RSR2000
    EM single particle entitySymmetry type: ASYMMETRIC
    3D reconstructionResolution: 14.9 A / CTF correction method: defocus groups / Details: The resolution is based on FSC at 0.5 cut-off
    Atomic model buildingMethod: normal mode-based flexible fitting / Software name: RSR2000
    Ref protocol: normal mode-based flexible fitting, real space refinement
    Ref space: REAL / Target criteria: correlation coefficient, R-factor
    Number of atoms included #LASTProtein: 1176 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1176

    +
    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