|Entry||Database: EMDB / ID: 6408|
|Title||In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus|
|Keywords||cryo-EM / dsRNA genome organization / viral polymerase|
|Sample||CPV VP4 + polymerase complex (TEC)|
|Source||Bombyx mori cypovirus 1 / virus / Cytoplasmic polyhedrosis virus / image: Bombyx mori|
|Map data||Averaged qCPV TEC|
|Method||single particle reconstruction, at 3.3 Å resolution|
|Authors||Zhang X / Ding K / Yu XK / Chang W / Sun JC / Zhou ZH|
|Citation||Nature, 2015, 527, 531-534|
|Validation Report||PDB-ID: 3jb6|
SummaryFull reportAbout validation report
|Date||Deposition: Aug 1, 2015 / Header (metadata) release: Aug 19, 2015 / Map release: Oct 28, 2015 / Last update: Dec 2, 2015|
Downloads & links
|File||emd_6408.map.gz (map file in CCP4 format, 11918 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.01 Å|
CCP4 map header:
-Entire CPV VP4 + polymerase complex (TEC)
|Entire||Name: CPV VP4 + polymerase complex (TEC) / Number of components: 2|
-Component #1: protein, VP4
|Protein||Name: VP4 / Recombinant expression: No|
|Source||Species: Bombyx mori cypovirus 1 / virus / Cytoplasmic polyhedrosis virus / image: Bombyx mori|
-Component #2: protein, RNA polymerase
|Sample solution||Buffer solution: 70 mM Tris-Cl, 10 mM MgCl2, 100 mM NaCl, 2 mM GTP|
|Support film||200 mesh Quantifoil holey carbon film|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Jul 26, 2013|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 49000 X (nominal), 49500 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 4500 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 4385 / Sampling size: 5 microns|
|Processing||Method: single particle reconstruction / Number of class averages: 1 / Applied symmetry: C1 (asymmetric) / Number of projections: 68526|
|3D reconstruction||Software: Frealign / CTF correction: Each particle / Resolution: 3.3 Å / Resolution method: FSC 0.143, semi-independent|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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