|Entry||Database: PDB / ID: 5x5b|
|Title||Prefusion structure of SARS-CoV spike glycoprotein, conformation 2|
|Keywords||VIRAL PROTEIN / SARS-CoV / spike glycoprotein / prefusion / single particle|
|Specimen source||SARS coronavirus BJ01 / virus|
|Method||Electron microscopy (3.7 Å resolution / Particle / Single particle)|
|Authors||Yuan, Y. / Cao, D. / Zhang, Y. / Ma, J. / Qi, J. / Wang, Q. / Lu, G. / Wu, Y. / Yan, J. / Shi, Y. / Zhang, X. / Gao, G.F.|
|Citation||Nat Commun, 2017, 8, 15092-15092|
Nat Commun, 2017, 8, 15092-15092 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Feb 15, 2017 / Release: May 3, 2017|
Downloads & links
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
Mass: 136825.891 Da / Num. of mol.: 3 / Source: (gene. exp.) SARS coronavirus BJ01 / virus
|Sequence details||THE REFERENCE SEQUENCE DATABASE OF THIS PROTEIN IS RESIDUES 14-1193 IN GENBANK AAP30030.1. RESIDUES 1194-1241 ARE EXPRESSION TAGS.|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: SARS-CoV spike trimer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: SARS coronavirus BJ01 / Strain: BJ01|
|Source (recombinant)||Organism: Spodoptera frugiperda|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: dev_2411: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000 / Symmetry type: POINT|
|Atomic model building||Ref protocol: RIGID BODY FIT|
|Atomic model building|
|Refine LS restraints|
-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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