|Entry||Database: EMDB / ID: 5172|
|Title||3.6 Angstrom cryoEM structure of human adenovirus type 5|
|Keywords||human adenovirus / cryoEM / 3D reconstruction / full-atom model / interaction network|
|Sample||human adenovirus type 5|
|Source||Human adenovirus 5 / virus / human adenovirus type 5|
|Map data||The cryoEM density map is for a huge virus (920A in diameter)and the size is 2.4GB.|
|Method||single particle (icosahedral) reconstruction, at 3.6 Å resolution|
|Authors||Liu H / Jin L / Koh SBS / Atanasov I / Schein S / Wu L / Zhou ZH|
|Citation||Science, 2010, 329, 1038-1043|
|Validation Report||PDB-ID: 3iyn|
About validation report
|Date||Deposition: Mar 9, 2010 / Header (metadata) release: May 21, 2010 / Map release: Sep 1, 2010 / Last update: Sep 6, 2011|
Downloads & links
|File||emd_5172.map.gz (map file in CCP4 format, 1242298 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire human adenovirus type 5
|Entire||Name: human adenovirus type 5|
Details: 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.
Number of components: 15 / Oligomeric State: Icosahedral particle
-Component #1: virus, Human adenovirus 5
|Virus||Name: Human adenovirus 5 / a.k.a: human adenovirus type 5 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE|
|Mass||Theoretical: 150 MDa / Experimental: 150 MDa|
|Species||Species: Human adenovirus 5 / virus / human adenovirus type 5|
|Source (natural)||Host Species: Homo sapiens / human / Host category: VERTEBRATES|
|Sample solution||Buffer solution: 10mM Tris-HCL,1mM MgCl2 / pH: 7.5|
|Support film||200 mesh holey carbon grid|
|Staining||The virus particles were not stained.|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging|
Details: Vitrification instrument: FEI Vitrobot. Vitrification carried out in a chamber with controlled humidity.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: May 1, 2009 / Details: low-dose|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
|Specimen Holder||Holder: Eucentric / Model: OTHER / Temperature: 90 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 756 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8|
|Processing||Method: single particle (icosahedral) reconstruction|
Details: 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.
Number of projections: 31815 / Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: common lines / Software: IMIRS / CTF correction: Each particle|
Details: 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.
Resolution: 3.6 Å / Resolution method: FSC 0.5
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