Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2j28: MODEL OF E. COLI SRP BOUND TO 70S RNCS -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 2j28
    TitleMODEL OF E. COLI SRP BOUND TO 70S RNCS
    DescriptorSIGNAL SEQUENCE
    SIGNAL RECOGNITION PARTICLE 54
    (50S ribosomal protein ...) x 28
    KeywordsRIBOSOME / PROTEIN-RNA COMPLEX / SIGNAL RECOGNITION PARTICLE
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron microscopy (8 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHalic, M. / Blau, M. / Becker, T. / Mielke, T. / Pool, M.R. / Wild, K. / Sinning, I. / Beckmann, R.
    CitationNature, 2006, 444, 507-511

    Nature, 2006, 444, 507-511 StrPapers
    Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
    Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann

    DateDeposition: Aug 16, 2006 / Release: Nov 8, 2006 / Last modification: Oct 20, 2010

    -
    Structure visualization

    Movie
    • Deposited structure unit
    • 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
    0: 50S RIBOSOMAL PROTEIN L32
    1: 50S RIBOSOMAL PROTEIN L33
    2: 50S RIBOSOMAL PROTEIN L34
    3: 50S RIBOSOMAL PROTEIN L35
    4: 50S RIBOSOMAL PROTEIN L36
    7: SIGNAL SEQUENCE
    8: 4.5S SIGNAL RECOGNITION PARTICLE RNA
    9: SIGNAL RECOGNITION PARTICLE 54
    A: 5S RIBOSOMAL RNA
    B: 23S RIBOSOMAL RNA
    C: 50S RIBOSOMAL PROTEIN L2
    D: 50S RIBOSOMAL PROTEIN L3
    E: 50S RIBOSOMAL PROTEIN L4
    F: 50S RIBOSOMAL PROTEIN L5
    G: 50S RIBOSOMAL PROTEIN L6
    H: 50S RIBOSOMAL PROTEIN L9
    I: 50S RIBOSOMAL PROTEIN L11
    J: 50S RIBOSOMAL PROTEIN L13
    K: 50S RIBOSOMAL PROTEIN L14
    L: 50S RIBOSOMAL PROTEIN L15
    M: 50S RIBOSOMAL PROTEIN L16
    N: 50S RIBOSOMAL PROTEIN L17
    O: 50S RIBOSOMAL PROTEIN L18
    P: 50S RIBOSOMAL PROTEIN L19
    Q: 50S RIBOSOMAL PROTEIN L20
    R: 50S RIBOSOMAL PROTEIN L21
    S: 50S RIBOSOMAL PROTEIN L22
    T: 50S RIBOSOMAL PROTEIN L23
    U: 50S RIBOSOMAL PROTEIN L24
    V: 50S RIBOSOMAL PROTEIN L25
    W: 50S RIBOSOMAL PROTEIN L27
    X: 50S RIBOSOMAL PROTEIN L29
    Y: 50S RIBOSOMAL PROTEIN L30
    Z: 50S RIBOSOMAL PROTEIN L31
    hetero molecules

    1.43 MDa, 145 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,428,781145
    Polyers1,426,08334
    Non-polymers2,698111
    Water9,224512

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

    -
    Components

    +
    50S ribosomal protein ... , 29 types, 29 molecules 01234CDEFG...

    #1polypeptide(L) / 50S RIBOSOMAL PROTEIN L32 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7N4
    #2polypeptide(L) / 50S RIBOSOMAL PROTEIN L33 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7N9
    #3polypeptide(L) / 50S RIBOSOMAL PROTEIN L34 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7P5
    #4polypeptide(L) / 50S RIBOSOMAL PROTEIN L35 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7Q2
    #5polypeptide(L) / 50S RIBOSOMAL PROTEIN L36 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7Q6
    #11polypeptide(L) / 50S RIBOSOMAL PROTEIN L2 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P60422
    #12polypeptide(L) / 50S RIBOSOMAL PROTEIN L3 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P60438
    #13polypeptide(L) / 50S RIBOSOMAL PROTEIN L4 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P60723
    #14polypeptide(L) / 50S RIBOSOMAL PROTEIN L5 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P62399
    #15polypeptide(L) / 50S RIBOSOMAL PROTEIN L6 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AG55
    #16polypeptide(L) / 50S RIBOSOMAL PROTEIN L9 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7R1
    #17polypeptide(L) / 50S RIBOSOMAL PROTEIN L11 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7J7
    #18polypeptide(L) / 50S RIBOSOMAL PROTEIN L13 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AA10
    #19polypeptide(L) / 50S RIBOSOMAL PROTEIN L14 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0ADY3
    #20polypeptide(L) / 50S RIBOSOMAL PROTEIN L15 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P02413
    #21polypeptide(L) / 50S RIBOSOMAL PROTEIN L16 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0ADY7
    #22polypeptide(L) / 50S RIBOSOMAL PROTEIN L17 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AG44
    #23polypeptide(L) / 50S RIBOSOMAL PROTEIN L18 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0C018
    #24polypeptide(L) / 50S RIBOSOMAL PROTEIN L19 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7K6
    #25polypeptide(L) / 50S RIBOSOMAL PROTEIN L20 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7L3
    #26polypeptide(L) / 50S RIBOSOMAL PROTEIN L21 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AG48
    #27polypeptide(L) / 50S RIBOSOMAL PROTEIN L22 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P61175
    #28polypeptide(L) / 50S RIBOSOMAL PROTEIN L23 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0ADZ0
    #29polypeptide(L) / 50S RIBOSOMAL PROTEIN L24 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P60624
    #30polypeptide(L) / 50S RIBOSOMAL PROTEIN L25 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P68919
    #31polypeptide(L) / 50S RIBOSOMAL PROTEIN L27 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7L8
    #32polypeptide(L) / 50S RIBOSOMAL PROTEIN L29 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7M6
    #33polypeptide(L) / 50S RIBOSOMAL PROTEIN L30 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AG51
    #34polypeptide(L) / 50S RIBOSOMAL PROTEIN L31 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A7M9

    -
    Polypeptide(L) , 2 types, 2 molecules 79

    #6polypeptide(L) / SIGNAL SEQUENCE
    #8polypeptide(L) / SIGNAL RECOGNITION PARTICLE 54 / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0AGD7

    -
    RNA chain , 3 types, 3 molecules 8AB

    #7RNA chain / 4.5S SIGNAL RECOGNITION PARTICLE RNA / Source: ESCHERICHIA COLI (gene. exp.)
    #9RNA chain / 5S RIBOSOMAL RNA / Source: ESCHERICHIA COLI (gene. exp.)
    #10RNA chain / 23S RIBOSOMAL RNA / Source: ESCHERICHIA COLI (gene. exp.)

    -
    Non-polymers , 2 types, 623 molecules

    #35ChemComp-MG / MAGNESIUM ION
    #36ChemComp-HOH / water

    +
    Experimental details

    -
    Experiment

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

    -
    Sample preparation

    Assembly of specimenName: SRP BOUND TO 70S RNCS / Aggregation state: PARTICLE
    Specimen supportDetails: CARBON

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F30
    Electron gunAccelerating voltage: 300 kV
    Electron lensMode: BRIGHT FIELD
    Radiation wavelengthRelative weight: 1

    -
    Processing

    Image selectionSoftware name: SPIDER
    EM single particle entitySymmetry type: ASYMMETRIC
    Least-squares processHighest resolution: 8 A
    Refine hist #LASTHighest resolution: 8 A
    Number of atoms included #LASTProtein: 29643 / Nucleic acid: 65092 / Ligand: 111 / Solvent: 512 / Total: 95358

    +
    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