Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1612: Nanoscale DNA box -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1612
    TitleNanoscale DNA box
    KeywordsDNA box / origami / self-assembly / lid / nanoscale
    SampleDNA Box
    SourceSynthetic construct
    Map data3D Map of DNA Box
    Methodsingle particle reconstruction
    AuthorsAndersen ES / Dong M / Nielsen MM / Jahn K / Subramani R / Mamdouh W / Golas MM / Sander B / Stark H / Oliveira CL / Pedersen JS / Birkedal V / Besenbacher F / Gothelf KV / Kjems J
    CitationNature, 2009, 459, 73-76

    Nature, 2009, 459, 73-76 StrPapers
    Self-assembly of a nanoscale DNA box with a controllable lid.
    Ebbe S Andersen / Mingdong Dong / Morten M Nielsen / Kasper Jahn / Ramesh Subramani / Wael Mamdouh / Monika M Golas / Bjoern Sander / Holger Stark / Cristiano L P Oliveira / Jan Skov Pedersen / Victoria Birkedal / Flemming Besenbacher / Kurt V Gothelf / Jørgen Kjems

    DateDeposition: Mar 28, 2009 / Header (metadata) release: Apr 15, 2009 / Map release: Apr 26, 2011 / Last update: Mar 28, 2009

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.065
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.065
    • 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_1612.map.gz (map file in CCP4 format, 2001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    80 pix
    9.8 A/pix
    = 784. A
    80 pix
    9.8 A/pix
    = 784. A
    80 pix
    9.8 A/pix
    = 784. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 9.8 A
    Density
    Contour Level:0.065 (by author), 0.065 (movie #1):
    Minimum - Maximum-0.20561 - 0.320627
    Average (Standard dev.)0.00281696 (0.0380516)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions808080
    Origin000
    Limit797979
    Spacing808080
    CellA=B=C: 784 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z9.89.89.8
    M x/y/z808080
    origin x/y/z0.0000.0000.000
    length x/y/z784.000784.000784.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-17-17-200
    NX/NY/NZ123123401
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS808080
    D min/max/mean-0.2060.3210.003

    -
    Supplemental data

    -
    Sample components

    -
    Entire DNA Box

    EntireName: DNA Box / Number of components: 1

    -
    Component #1: nucleic-acid, DNA box

    Nucleic-acidName: DNA box / a.k.a: DNA box / Class: DNA / Structure: DOUBLE HELIX / Synthetic: Yes
    SourceSpecies: Synthetic construct

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: ETHANE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: SPOT SCAN
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Side Entry Eucentric / Model: GATAN LIQUID NITROGEN

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral)

    +
    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