Sandbox GGC3: Difference between revisions

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==Spike glycoprotein==

3D structure representation of the Spike glycoprotein related to the SARS-CoV-2 <ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref>.

==Introduction==

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==Activation of S-protein==

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

[[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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LYS 187 <scene name='75/752266/Lys_187/1'>The Receptor Binding Domain (RBD)</scene>

[[Image:Picture3.jpg]]<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>

[[Image:Picture3.jpg]]<ref>doi:10.1038/s41401-020-0485-4</ref>

==Mutation==

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>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>.

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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== Structural highlights ==

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>

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>

</StructureSection>

Sandbox GGC3: Difference between revisions

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@@ Line 1: / Line 1: @@
 ==Spike glycoprotein==
 <StructureSection load='6VSB' size='340' side='right' caption='3D representation of the Spike glycoprotein' scene=''>
 D structure representation of the Spike glycoprotein related to the SARS-CoV-2 <ref>DOI 10.1002/ijch.201300024</ref>  <ref>PMID:21638687</ref>.
 ==Introduction==
@@ Line 16: / Line 16: @@
 ==Activation of S-protein==
- 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
+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
 [[Image:Cleavage.jpg]] <ref>Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., &amp; 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>
@@ Line 23: / Line 23: @@
 LYS 187 <scene name='75/752266/Lys_187/1'>The Receptor Binding Domain (RBD)</scene>
-[[Image:Picture3.jpg]]<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>
+[[Image:Picture3.jpg]]<ref>doi:10.1038/s41401-020-0485-4</ref>
 ==Mutation==
- 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>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>.
+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>.
@@ Line 34: / Line 34: @@
 == Structural highlights ==
-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>
+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>
 </StructureSection>