3D structural studies on SARS-CoV-2

From Proteopedia

SARS-CoV-2 virus. The spikes, that adorn the virus surface, impart a corona like appearance (Fusion Animation).

The genome of the SARS-CoV-2 virus codes for 28 proteins: Out of those, 19 have already been characterized structurally. For the rest there are accurate AlphaFold2 predicted structures.
Details of the 3D structure & function of the key proteins & RNA inside the virus can be seen in the NY Times^[1]. "The first viral protein created inside the infected cell, ORF1ab, is actually a chain of 16 proteins joined together. Two of these proteins act like scissors, snipping the links between the different proteins and freeing them to do their jobs."^[1]

SARS-CoV-2 Protein Organization, redrawn from NY Times^[1]

• Main protease: it is a cysteine protease that is essential for the viral life cycle.
• NSP1: Host translation inhibitor nsp1. Inhibits host translation by interacting with the 40S ribosomal subunit.
• NSP2: Non-structural protein 2.
• Papain-like proteinase
• NSP4: Non-structural protein 4.
• Proteinase 3CL-PRO
• AlphaFold2 Theoretical Model NSP6: Non-structural protein 6.
• NSP7: Non-structural protein 7.
• NSP8: Non-structural protein 8.
• NSP9: Non-structural protein 9.
• NSP10: Non-structural protein 10.
• RNA-directed RNA polymerase (RdRp)
• Helicase (Hel): Multi-functional protein with a zinc-binding domain in N-terminus
• Guanine-N7 methyltransferase (ExoN)
• Uridylate-specific endoribonuclease (NendoU)
• 2'-O-methyltransferase (2'-O-MT): Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs.
• Surface glycoprotein (S) and SARS-CoV-2 protein S priming by furin
• ORF3a: Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release.
• Protein E: Plays a central role in virus morphogenesis and assembly.
• AlphaFold2 Theoretical Model Protein M: Component of the viral envelope.
• ORF6: Could be a determinant of virus virulence.
• ORF7a: Non-structural protein which is dispensable for virus replication in cell culture.
• ORF8: Open Reading Frame 8.
• AlphaFold2 Theoretical Model Protein N: Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP).
• AlphaFold2 Theoretical Model ORF10‎: It is currently unclear whether this region translates into a functional protein.

References

1. ↑ ^{1.0 1.1 1.2} NY Times (3-Apr-2020) Bad News Wrapped in Protein: Inside the Coronavirus Genome