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- EMDB-1612: Nanoscale DNA box -

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Basic information

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 Yorodumi Papers
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: Oct 24, 2012

Structure visualization

  • 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:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1612.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
9.8 Å/pix.
= 784. Å
80 pix
9.8 Å/pix.
= 784. Å
80 pix
9.8 Å/pix.
= 784. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 784 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
start NX/NY/NZ-17-17-200
MAP C/R/S123
start NC/NR/NS000
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)

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