Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2wfs: Fitting of influenza virus NP structure into the 9-fold symmetryz... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 2wfs
    TitleFitting of influenza virus NP structure into the 9-fold symmetryzed cryoEM reconstruction of an active RNP particle.
    DescriptorNUCLEOPROTEIN
    KeywordsVIRAL PROTEIN / VIRAL NUCLEOPROTEIN / HOST-VIRUS INTERACTION / RNA VIRUSES / NUCLEOPROTEIN / RIBONUCLEOPROTEIN / RNA / VIRION / NUCLEUS / INFLUENZA / RNA-BINDING
    Specimen sourceINFLUENZA A VIRUS / virus
    MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice cryo EM)
    AuthorsColoma, R. / Valpuesta, J.M. / Arranz, R. / Carrascosa, J.L. / Ortin, J. / Martin-Benito, J.
    CitationPLoS Pathog., 2009, 5, e1000491-e1000491

    PLoS Pathog., 2009, 5, e1000491-e1000491 StrPapers
    The structure of a biologically active influenza virus ribonucleoprotein complex.
    Rocío Coloma / José M Valpuesta / Rocío Arranz / José L Carrascosa / Juan Ortín / Jaime Martín-Benito

    DateDeposition: Apr 15, 2009 / Release: Jul 7, 2009 / Last modification: Dec 28, 2011

    -
    Structure visualization

    Movie
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • Biological unit as monomeric
    • Imaged by Jmol
    • Download
    • 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
    A: NUCLEOPROTEIN
    B: NUCLEOPROTEIN
    C: NUCLEOPROTEIN
    D: NUCLEOPROTEIN
    E: NUCLEOPROTEIN
    F: NUCLEOPROTEIN
    G: NUCLEOPROTEIN
    H: NUCLEOPROTEIN
    I: NUCLEOPROTEIN

    511 kDa, 9 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    511,2599
    Polyers511,2599
    Non-polymers00
    Water0

    Omokage search
    #1
    A: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #2
    B: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #3
    C: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #4
    D: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #5
    E: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #6
    F: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #7
    G: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #8
    H: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search
    #9
    I: NUCLEOPROTEIN

    defined by author&software (PISA) / 56.8 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    56,8071
    Polyers56,8071
    Non-polymers00
    Water0
    / Symmetry operations: (identity)x1
    Download / Omokage search

    -
    Components

    #1polypeptide(L) / NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN, PROTEIN N / Source: INFLUENZA A VIRUS (gene. exp.)

    +
    Experimental details

    -
    Experiment

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

    -
    Sample preparation

    Assembly of specimenName: INFLUENZA VIRUS RIBONUCLEOPROTEIN PARTICLE / Aggregation state: PARTICLE
    Details: MICROGRAPHS SELECTED BY COMPUTED CTF DATA AQUISITION
    Buffer solutionName: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE
    Sample preparationpH: 8
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: CRYOGEN - ETHANE INSTRUMENT - LEICA PLUNGER

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI G2
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Cs: 2.26 mm
    Specimen holderTemperature: 99 K
    CameraType: FILM (KODAK SO-136)
    EM image scansNumber digital images: 159

    -
    Processing

    Image selectionSoftware name: SPIDER / Number of particles: 9571
    EM single particle entitySymmetry type: MIXED SYMMETRY
    3D reconstructionMethod: ANGULAR RECONSTITUTION,ITERATIVE ALGEBRAIC RECONSTRUCTION
    Resolution: 12 A / Actual pixel size: 2.8 A/pix / CTF correction method: WHOLE PLATE
    Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1603.
    Atomic model buildingMethod: RIGID BODY / Ref space: RECIPROCAL / Target criteria: VOLUMETRIC
    Least-squares processHighest resolution: 12 A
    Refine hist #LASTHighest resolution: 12 A
    Number of atoms included #LASTProtein: 15336 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 15336

    +
    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