|Entry||Database: EMDB / ID: 5133|
|Title||17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure|
|Keywords||RHDV / vp60 / vp10 / core-like particles|
|Sample||wild Rabbit Hemorrhagic Disease Viruses core-like particles|
|Source||rabbit hemorrhagic disease virus core like particles / virus|
|Map data||This is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.|
|Method||single particle (icosahedral) reconstruction, at 17 Å resolution|
|Authors||Hu Z / Tian X / Zhai Y / Xu W / Zheng D / Sun F|
|Citation||Protein Cell, 2010, 1, 48-58|
|Date||Deposition: Oct 11, 2009 / Header (metadata) release: Oct 15, 2009 / Map release: Aug 12, 2010 / Last update: Jan 10, 2011|
Downloads & links
|File||emd_5133.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.54 Å|
CCP4 map header:
-Entire wild Rabbit Hemorrhagic Disease Viruses core-like particles
|Entire||Name: wild Rabbit Hemorrhagic Disease Viruses core-like particles|
Number of components: 3 / Oligomeric State: icosahedral
|Mass||Theoretical: 7.2 MDa|
-Component #1: virus, rabbit hemorrhagic disease virus core like particles
|Virus||Name: rabbit hemorrhagic disease virus core like particles / a.k.a: rabbit hemorrhagic disease virus core like particles / Class: VIROID / Empty: No / Enveloped: No / Isolate: SPECIES|
|Mass||Theoretical: 7.2 MDa|
|Species||Species: rabbit hemorrhagic disease virus core like particles / virus|
|Source (natural)||Host Species: Oryctolagus cuniculus / mammal / アナウサギ / |
Host category: VERTEBRATES
|Shell #1||Name of element: S / Diameter: 320 Å / T number(triangulation number): 3|
|Support film||300 mesh holygrid|
|Vitrification||Instrument: NONE / Cryogen name: ETHANE|
Method: Embeded in thin layer of vitreous ice on freshly carbon-coated home-made holey EM grid by manually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN HELIUM / Temperature: 105 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 230 / Sampling size: 12.7 microns / Bit depth: 16|
|Processing||Method: single particle (icosahedral) reconstruction / Number of class averages: 21 / Number of projections: 895 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: shadow matching method / Software: Eman spider / CTF correction: Each particle / Resolution: 17 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: chimera / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 2GH8
-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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