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Nanoscale DNA box

by single particle reconstruction

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.065, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.065, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1612
TitleNanoscale DNA box
Map3D Map of DNA Box
SampleDNA Box
KeywordsDNA box, origami, self-assembly, lid, nanoscale
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
DateDeposition: 2009-03-28, Header release: 2009-04-15, Map release: 2011-04-26, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.065, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.065, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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Search for similar-shape assemblies throgh:
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Article
Citation - Primary
ArticleNature, Vol. 459, Issue 7243, Page 73-6, Year 2009
TitleSelf-assembly of a nanoscale DNA box with a controllable lid.
AuthorsEbbe 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
Danish National Research Foundation: Centre for DNA Nanotechnology.
KeywordsCryoelectron Microscopy, DNA (chemistry, 9007-49-2), Imaging, Three-Dimensional, Microscopy, Atomic Force, Nanostructures (chemistry), Nucleic Acid Conformation
LinksDOI: 10.1038/nature07971, PubMed: 19424153
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.

Density
Contour Level:0.065 (by author), 0.065 (movie #1):
Minimum - Maximum: -0.20561 - 0.320627
Average (Standard dev.): 0.00281696 (0.0380516)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
Unit CellA= B= C: 784 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 9.8 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.2060.3210.003
Annotation Details3D Map of DNA Box
Supplement
Images
Images
Sample
NameDNA Box
Number of Components1
Component #1: nucleic-acid - DNA box
Scientific nameDNA box
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
StructureDOUBLE HELIX
ClassDNA
SyntheticYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage160 kV
Illumination ModeSPOT SCAN
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderSide Entry Eucentric
ModelGATAN LIQUID NITROGEN
Camera
Processing
Methodsingle particle reconstruction
Single Particle
Applied SymmetryD2 (2*2 fold dihedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1612.xml (5.1 KB)
Map dataemd_1612.map.gz (1.6 MB)
Imagesem1612.png (203.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1612
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.4 KB