|Entry||Database: EMDB / ID: 7094|
|Title||Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections|
|Sample||Porcine deltacoronavirus spike glycoprotein|
|Source||Porcine deltacoronavirus / virus|
|Map data||deltacoronavirus spike glycoprotein|
|Method||single particle reconstruction, at 3.5 Å resolution|
|Authors||Xiong X / Tortorici MA|
|Citation||J. Virol., 2017|
J. Virol., 2017 Yorodumi Papers
|Validation Report||PDB-ID: 6bfu|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 27, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Dec 6, 2017|
Downloads & links
|File||emd_7094.map.gz (map file in CCP4 format, 131073 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.33 Å|
CCP4 map header:
+Entire Porcine deltacoronavirus spike glycoprotein
|Entire||Name: Porcine deltacoronavirus spike glycoprotein / Number of components: 5|
+Component #1: protein, Porcine deltacoronavirus spike glycoprotein
|Protein||Name: Porcine deltacoronavirus spike glycoprotein / Recombinant expression: No|
|Source||Species: Porcine deltacoronavirus / virus|
|Source (engineered)||Expression System: Drosophila melanogaster / arthropod / キイロショウジョウバエ /|
+Component #2: protein, Spike protein
|Protein||Name: Spike protein / Recombinant expression: No|
|Mass||Theoretical: 112.514773 kDa|
|Source (engineered)||Expression System: Porcine deltacoronavirus / virus|
+Component #3: ligand, N-ACETYL-D-GLUCOSAMINE
|Ligand||Name: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 102 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
+Component #4: ligand, BETA-D-MANNOSE
|Ligand||Name: BETA-D-MANNOSE / Number of Copies: 33 / Recombinant expression: No|
|Mass||Theoretical: 0.180156 kDa|
+Component #5: ligand, ALPHA-D-MANNOSE
|Ligand||Name: ALPHA-D-MANNOSE / Number of Copies: 33 / Recombinant expression: No|
|Mass||Theoretical: 0.180156 kDa|
|Sample solution||Specimen conc.: 0.5 mg/ml / pH: 8|
|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: 40 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 / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 455710|
|3D reconstruction||Software: RELION / Resolution: 3.5 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
Major update of PDB
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