|Entry||Database: EMDB / ID: 7063|
|Title||Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state|
|Sample||Porcine delta coronavirus spike trimer in the pre-fusion state|
|Source||Deltacoronavirus PDCoV/USA/Ohio137/2014 / virus|
|Map data||Delta coronavirus spike protein in the pre-fusion state|
|Method||single particle reconstruction, at 3.3 Å resolution|
|Authors||Shang J / Zheng Y / Yang Y / Liu C / Geng Q / Tai W / Du L / Zhou Y / Zhang W / Li F|
|Citation||J. Virol., 2017|
|Validation Report||PDB-ID: 6b7n|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 4, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Nov 8, 2017|
Downloads & links
|File||emd_7063.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.3 Å|
CCP4 map header:
-Entire Porcine delta coronavirus spike trimer in the pre-fusion state
|Entire||Name: Porcine delta coronavirus spike trimer in the pre-fusion state|
Number of components: 3
-Component #1: protein, Porcine delta coronavirus spike trimer in the pre-fusion...
|Protein||Name: Porcine delta coronavirus spike trimer in the pre-fusion state|
Recombinant expression: No
|Source||Species: Deltacoronavirus PDCoV/USA/Ohio137/2014 / virus|
|Source (engineered)||Expression System: Spodoptera frugiperda / arthropod|
-Component #2: protein, Spike protein
|Protein||Name: Spike protein / Recombinant expression: No|
|Mass||Theoretical: 122.277266 kDa|
|Source (engineered)||Expression System: Deltacoronavirus PDCoV/USA/Ohio137/2014 / virus|
-Component #3: ligand, N-ACETYL-D-GLUCOSAMINE
|Ligand||Name: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 57 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Sample solution||Specimen conc.: 0.35 mg/ml / pH: 7.2|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 87002|
|3D reconstruction||Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF|
-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
-Jul 12, 2017. Major update of PDB
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