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| - | ==Spike glycoprotein== | + | ==Name of your Protein== |
| - | <StructureSection load='6VSB' size='340' side='right' caption='3D representation of the Spike glycoprotein' scene=''> | + | <StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''> |
| - | 3D structure representation of the Spike glycoprotein related to the SARS-CoV-2 <ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref>.
| + | This is a default text for your page. Click above on '''edit this page''' to modify. Be careful with the < and > signs. |
| | + | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. |
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| - | ==Introduction== | + | == Function == |
| - | The Spike protein is related to the novel coronavirus pandemic discovered in 2019. The virus is named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and it belongs to the β coronavirus family. The SARS-CoV-2 is a single stranded RNA with 29,881bp length, which encodes for 9860 amino acids. It is compose of two proteins: the structural and non-structural proteins. The structural proteins are S,E,M and N ; whiles as the non-structural proteins are encoded on the ORF regions<ref>Huang, Y., Yang, C., Xu, X., Xu, W., & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141-1149. doi:10.1038/s41401-020-0485-4</ref>.
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| - | ==The Spike Protein==
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| - | The S-protein is a structural protein extends from the viral membrane and it is uniformly arranged as a trimer on the surface to give the crown-like appearance of the SARS-Co
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| - | V-2. The Spike protein is 14-1255bp long, which mediates a receptor binding Val367<scene name='75/752266/Val367/1'>Binding region val367</scene> and fusion of the virus and a cellular membrane <ref>Mohammad, A., Alshawaf, E., Marafie, S. K., Abu-Farha, M., Abubaker, J., & Al-Mulla, F. (2020). Higher binding affinity of Furin to SARS-CoV-2 spike (S) protein D614G could be associated with higher SARS-CoV-2 infectivity. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, S1201-9712(20)32237-2. Advance online publication. https://doi.org/10.1016/j.ijid.2020.10.033</ref>. Is also gives the virus its name in Latin as "Corona".
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| - | ==Domains==
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| - | The S-protein of the SARS-CoV-2 has two main subunits , an S1 and S2 subunits NTD-CT<scene name='75/752266/Ntd_-_ct/1'>S1 subunit is in the downstream of NTD and S2 subunit is in the upsteam of CT</scene> . The S1 subunit is located on residue #14–685 ( contains the NTD, blue label) and interact with human AEC2 by attaching its virion to the cell membrane by interacting with host receptor. The S2 subunit is located on residue #686–1273 ( contains the CT, red label ) which serves as the fusion protein of the virus <ref>UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. (2020, October 07). Spike glycoprotein. Retrieved November 13, 2020, from https://www.uniprot.org/uniprot/P59594</ref>.
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| - | ==Activation of S-protein==
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| - | Before the Spike protein can be activated , it has to be cleaved by the protease Furin protein ALA 668 <scene name='75/752266/Ala_668/1'>Furin Cleavage site</scene> . This 2D image below shows the schematic cleavage of the S-protein before and after it enters the host cell
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| - | [[Image:Cleavage.jpg]] <ref>Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020, May 26). Cell entry mechanisms of SARS-CoV-2. Retrieved November 14, 2020, from https://www.pnas.org/content/117/21/11727</ref>
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| - | ==The Mechanism of the Spike Protein==
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| - | LYS 187 <scene name='75/752266/Lys_187/1'>The Receptor Binding Domain (RBD)</scene>
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| - | [[Image:Picture3.jpg]]<ref>doi:10.1038/s41401-020-0485-4</ref>
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| - | ==Mutation==
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| - | The most studied mutation site of the S-protein is at residue 614 which encodes for the amino acid Aspartic acid (D) D614 <scene name='75/752266/Asp_614/1'>The Mutation site D614 </scene> and is normally changed to Glycine (G). And this form of mutation causes the enhancement of the viral transmission <ref>doi.org/10.1016/j.ijid.2020.10.033</ref>.
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| | + | == Disease == |
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| | + | == Relevance == |
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| | == Structural highlights == | | == Structural highlights == |
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| - | These are the structural 3D representations of the s-protein showing the two subunits , the binding regions to its receptor human ACE2 , Mutation site , RBD site and cleavage site respectively. NTD-CT<scene name='75/752266/Ntd_-_ct/1'>S1 subunit is in the downstream of NTD and S2 subunit is in the upsteam of CT</scene> .Val367<scene name='75/752266/Val367/1'>Binding region val367</scene> . D614 <scene name='75/752266/Asp_614/1'>The Mutation site D614 </scene>. LYS 187 <scene name='75/752266/Lys_187/1'>The Receptor Binding Domain (RBD)</scene>.ALA 668 <scene name='75/752266/Ala_668/1'>Furin Cleavage site</scene>
| + | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. |
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| | </StructureSection> | | </StructureSection> |
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| | == References == | | == References == |
| | <references/> | | <references/> |
