2019-12-25 REL RCSB RCSB RCSB 2017-12-06 2018-01-24 2018-02-21 2019-12-25 National Science Foundation (NSF, United States) DMR-1344290 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM104427 United States National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) R01HL115153 United States Department of Energy (DOE, United States) DE-AC02-05CH11231 United States Single-Molecule 3D Image of DNA Origami Bennett Linkage by Individual Particle Electron Tomography (No. 088) Lei D Marras A Liu J Huang C Zhou L Castro C Su H Ren G Lei D Marras AE Liu J Huang CM Zhou L Castro CE Su HJ Ren G Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. Nat Commun UK 9 592 592 2018 29426880 doi:10.1038/s41467-018-03018-0 2041-1723 EMD-7204 associated EM volume
Conformation of a DNA origami Bennett linkage (No. 01)
 DNA origami Bennett linkage DNA origami Bennett linkage 0 M13 phage genome segment 1 Escherichia virus M13 Escherichia coli Synthetic DNA oligonucleotides 1 synthetic construct Escherichia coli tomography particle 7.5
Tris-Borate-EDTA (TBE) buffer containing 11 mM MgCl2
 NEGATIVE Uranyl Formate
The grid was washed twice by 1% (w/v) uranyl formate
 COPPER 200 CARBON LACEY GLOW DISCHARGE AIR 0.039 ETHANE 90 277 LEICA EM GP
DNA origami Bennett linkage was diluted to ~2 nM with Tris-Borate-EDTA (TBE) buffer containing 11 mM MgCl2
NO SECTIONING ZEISS LIBRA120PLUS FLOOD BEAM BRIGHT FIELD LAB6 120 2.2 50000.0 GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN In-column Omega Filter GATAN ULTRASCAN 4000 (4k x 4k) 4096 4096 1.76 1
X-ray speckles in images were removed before alignment and 3D reconstruction.
FOURIER SPACE 108.3 FSC 0.5 CUT-OFF
The 3D reconstruction was performed by using Individual-Particle Electron Tomography (IPET). The obtained 3D map was Gaussian low-pass filtered to 8 nm
57 emd_7204.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 921.60004 921.60004 921.60004 90.0 90.0 90.0 X Y Z -0.2237675 1.265378 0.01433586 0.09415065 4.8 4.8 4.8 AUTHOR primary map