Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1048: Three-dimensional structure of bacteriophage T4 baseplate. -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1048
    TitleThree-dimensional structure of bacteriophage T4 baseplate.
    SampleBacteriophage T4 baseplate-tail tube assembly
    SourceEnterobacteria phage T4 / virus / bacteriophage T4
    Map datamap contains the baseplate and the proximal part of the tail tube
    Methodsingle particle reconstruction, at 12 A resolution
    AuthorsKostyuchenko VA / Leiman PG / Chipman PR / Kanamaru S / vanRaaij MJ / Arisaka F / Mesyanzhinov VV / Rossmann MG
    CitationNat. Struct. Biol., 2003, 10, 688-693

    Nat. Struct. Biol., 2003, 10, 688-693 StrPapers
    Three-dimensional structure of bacteriophage T4 baseplate.
    Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann

    DateDeposition: May 19, 2003 / Header (metadata) release: May 19, 2003 / Map release: Sep 19, 2003 / Last update: May 19, 2003

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 2
    • 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_1048.map.gz (map file in CCP4 format, 29414 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    196 pix
    2.98 A/pix
    = 583.829 A
    196 pix
    2.98 A/pix
    = 583.829 A
    196 pix
    2.98 A/pix
    = 583.829 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.97872 A
    Density
    Contour Level:1.45 (by author), 2 (movie #1):
    Minimum - Maximum-7.64827013 - 10.34481144
    Average (Standard dev.)0E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions196196196
    Origin-98-98-97
    Limit979798
    Spacing196196196
    CellA=B=C: 583.8291 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.97871938775512.97871938775512.9787193877551
    M x/y/z196196196
    origin x/y/z0.0000.0000.000
    length x/y/z583.829583.829583.829
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ0052
    NX/NY/NZ12812855
    MAP C/R/S123
    start NC/NR/NS-98-98-97
    NC/NR/NS196196196
    D min/max/mean-7.64810.3450.000

    -
    Supplemental data

    -
    Sample components

    -
    Entire Bacteriophage T4 baseplate-tail tube assembly

    EntireName: Bacteriophage T4 baseplate-tail tube assembly / Number of components: 1 / Oligomeric State: the complex has sixfold symmetry

    -
    Component #1: protein, baseplate-tail tube complex

    ProteinName: baseplate-tail tube complex / Recombinant expression: Yes
    SourceSpecies: Enterobacteria phage T4 / virus / bacteriophage T4 / Strain: T4 18-,23-
    Source (engineered)Expression System: Escherichia coli be / bacteria / image: Escherichia coli
    Source (natural)Organelle: baseplate and tail tube

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 5 mg/ml / Buffer solution: water / pH: 7
    Support filmholey carbon
    VitrificationCryogen name: ETHANE / Method: Blot for 2 seconds before plunging

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 45000 X (nominal), 47000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 5000 nm
    Specimen HolderHolder: 626 Single Tilt Cryotransfer System / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8
    Details: images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 945 / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionAlgorithm: model based projection matching / Software: SPIDER / CTF correction: each particle
    Details: modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
    Resolution: 12 A / Resolution method: FSC 0.5

    -
    Atomic model buiding

    Modeling #1Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #2Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #3Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #4Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #5Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #6Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #7Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    Modeling #8Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
    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