2017-09-27 OBS 2010-03-09 RCSB RCSB 2010-05-21 2010-09-01 2017-09-27
Authors have produced a higher resolution map (EMD-7034).
3.6 Angstrom cryoEM structure of human adenovirus type 5 Liu H, Jin L, Koh SBS, Atanasov I, Schein S, Wu L, Zhou ZH human adenovirus, cryoEM, 3D reconstruction, full-atom model, interaction network 3iyn Liu H, Jin L, Koh SB, Atanasov I, Schein S, Wu L, Zhou ZH Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks. SCIENCE 329 1038 1043 2010 20798312 doi:10.1126/science.1187433 emd_5172.map.gz Image stored as Reals 860 860 430 -430 -430 0 429 429 429 860 860 430 946.0 946.0 473.0 90.0 90.0 90.0 X Y Z -37.94063568 48.27219391 0.13295805 3.91269684 1
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1.1 1.1 1.1 8.0 The cryoEM density map is for a huge virus (920A in diameter)and the size is 2.4GB. 15 human adenovirus type 5 Icosahedral particle
E1B gene-attenuated oncolytic human adenovirus type 5 was propagated in HEK 293 cells, harvested and liberated by 3 cycles of freezing-thawing and purified by CsCl step gradient ultra-centrifugation. The virion particles were then dialyzed and resuspended in 10 mM Tris (pH 7.5), 1 mM MgCl2.
virus Human adenovirus 5 human adenovirus type 5 150 150 Human adenovirus 5 human adenovirus type 5 false false SEROTYPE VIRION Homo sapiens VERTEBRATES 920 Blot for 4 seconds before plunging ETHANE
Vitrification instrument: FEI Vitrobot. Vitrification carried out in a chamber with controlled humidity.
100 FEI VITROBOT 90 objective lens astigmatism was corrected at 100,000 times magnification FIELD EMISSION GUN 20 BRIGHT FIELD 1000 2500 FLOOD BEAM Eucentric
low-dose
KODAK SO-163 FILM 2.7 0 0 90 FEI TITAN KRIOS 01-May-2009 0 OTHER 300 59000 NIKON SUPER COOLSCAN 9000 756 6.35 8 The virus particles were not stained. 200 mesh holey carbon grid particle
10mM Tris-HCL,1mM MgCl2
7.5 singleParticle common lines IMIRS Each particle
The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. We determined particle orientation, centre parameters and subsequent 3D reconstruction with the IMIRS package, enhanced by icosahedral symmetry-adapted functions for 3D reconstruction. We incorporated astigmatism in the CTF correction in both orientation-centre refinement and 3D reconstruction steps. The IMIRS procedure was optimized, and the data processing was completed within two months by three personal computers, each with eight 2.33GHz CPUs and 16G memory.
3.6 FSC 0.5
756 micrographs that clearly showed signals up to 4 Angstrom in their power spectra were selected. Individual particle images (1024 pixel by 1024 pixel) were first boxed out automatically by the autoBox program in the IMIRS package, followed by manual screening with the EMAN boxer program to keep only the well-separated, contamination-free and intact 45000 particles. The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. Determination of particle orientation and centre, and subsequent 3D reconstruction were done with the IMIRS package, enhanced by icosahedral symmetry-adapted functions.
31815 I