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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Introduction
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is an RNA virus that is responsible for the highly infectious respiratory disease, COVID-19.
Overall SARS-CoV-2 Structure
It is made up of four structural proteins: spike, envelope, membrane, and nucleocapsid proteins. The spike protein helps the virus infect human cells. The envelope protein helps in virus assembly and release. The membrane protein shapes the viral envelope. The nucleocapsid protein binds the RNA genome for replication. Once inside the cell, virus-specific RNA and proteins are synthesized within the cytoplasm. The viral envelope merges with the oily membrane of our own cells, allowing the virus to release its genetic material into the inside of the healthy cell. The genetic blueprint of the virus is RNA instead of DNA so it gives infected host cells instructions to read the template and translate it to replicate the virus. Each infected cell may produce and release millions of copies of the virus which can infect other neighboring cells and people when the viral particles are released from the airways (i.e., via coughing or sneezing).
Spike Protein
[1]
The spike protein is a glycoprotein that lies on the surface of SARS-CoV-2 to facilitate the entry of the virus into host cells. More specifically, once SARS-CoV-2 has entered the respiratory system, its spike protein binds to the ACE2 receptor (Angiotensin Converting Enzyme Receptor 2) in the lungs. The spike protein is cleaved into two functional subunits: S1 and S2. S1 contains the RBDs (receptor binding domains). S2 plays a key role in membrane fusion between the virus and host cell, allowing viral RNA to enter.
Receptor Binding Domains
The spike protein’s RBDs attach to the human ACE2 receptor.
ACE2 Receptor
ACE2 Binding Residues
AHB2
AHB2 Interactions
LCB
LCB1
LCB3
Binding Interactions
Function
[3]
[4]
Therapeutic Relevance
[3]
[4]
References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ 3.0 3.1 Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn(2+) /Mn(2+) heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017, Jun 14. PMID:28504306 doi:http://dx.doi.org/10.1002/1873-3468.12677
- ↑ 4.0 4.1 Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19. Int J Mol Sci. 2022 Feb 2;23(3):1716. PMID:35163638 doi:10.3390/ijms23031716
Student Contributors
- Carson Powers
- Rachael Vavul
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