3D structural studies on SARS-CoV-2

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

The quality of SARS-CoV-2 experimentally determined structures varies widely (Grabowski et al., 2021). Validated and corrected structures can be obtained from COVID19.BioReproducibility.Org.

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

3D structural studies on SARS-CoV-2 virus

  • A team of Chinese scientists determined, by Cryo-EM, the coronavirus spike receptor-binding domain complexed with its receptor ACE2 PDB-ID 6lzg (To be published).
  • A team of US and Chinese scientists determined the crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2 6m0j
  • Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 6w41
  • Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2 6w61 (To be published).
  • Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP 6w6y (To be published).
  • Structure of NSP10 - NSP16 Complex from SARS-CoV-2 6w75 (To be published).
  • Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain 6m3m (To be published).
  • Crystal structure of Nsp9 RNA binding protein of SARS CoV-2 6w4b (To be published).
  • Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 6w4h (To be published).
  • A Cryo-EM study by Zhou & colleagues on the structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2 gives insights to the molecular basis for coronavirus recognition and infection[3] 6m17.
  • Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 6vyo (To be published).
  • Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate 6w01 (To be published).
  • Crystal structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose 6w02 (To be published).
  • Crystal structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 6vw1
  • Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 6vww (To be published).
  • Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 6vxs (To be published).
  • Crystal structure of the 2019-nCoV HR2 Domain 6lvn (To be published).
  • Crystal structure of post fusion core of 2019-nCoV S2 subunit 6lxt.
  • Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors, from the Hilgenfeld lab[4], Apo Struture: PDB-ID 6y2e, and complexes with inhibitors: PDB-ID 6y2f and 6y2g.
  • 3D Structure of RNA-dependent RNA polymerase from COVID-19, a major antiviral drug target from the Rao lab in Beijing[5].
  • Crystal structure of the Mpro from COVID-19 and discovery of inhibitors in a study by scientists from Shanghai & Beijing[6], PDB-ID 6lu7.
  • Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 in a study by scientists from USA[7], PDB-ID 6w01.
  • The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. A study by McLellan and colleagues in "Science" on the Cryo-EM structure of the COVID-19 spike protein. This structure should greatly aid in the rapid development and evaluation of medical countermeasures to address the ongoing public health crisis[8], PDB-ID 6vsb.

References

  1. ↑ 1.0 1.1 1.2 NY Times (3-Apr-2020) Bad News Wrapped in Protein: Inside the Coronavirus Genome
  2. ↑ Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020 Mar 6. pii: S0092-8674(20)30262-2. doi: 10.1016/j.cell.2020.02.058. PMID:32155444 doi:http://dx.doi.org/10.1016/j.cell.2020.02.058
  3. ↑ Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science. 2020 Mar 4. pii: science.abb2762. doi: 10.1126/science.abb2762. PMID:32132184 doi:http://dx.doi.org/10.1126/science.abb2762
  4. ↑ Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science. 2020 Mar 20. pii: science.abb3405. doi: 10.1126/science.abb3405. PMID:32198291 doi:http://dx.doi.org/10.1126/science.abb3405
  5. ↑ Gao, et al. Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target: bioRxiv (online) 2020 http://doi.org/10.1101/2020.03.16.993386
  6. ↑ Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B, Li X, Zhang L, Peng C, Duan Y, Yu J, Wang L, Yang K, Liu F, Jiang R, Yang X, You T, Liu X, Yang X, Bai F, Liu H, Liu X, Guddat LW, Xu W, Xiao G, Qin C, Shi Z, Jiang H, Rao Z, Yang H. Structure of M(pro) from COVID-19 virus and discovery of its inhibitors. Nature. 2020 Apr 9. pii: 10.1038/s41586-020-2223-y. doi:, 10.1038/s41586-020-2223-y. PMID:32272481 doi:http://dx.doi.org/10.1038/s41586-020-2223-y
  7. ↑ Kim, et al. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2: bioRxiv (online) 2020 http://doi.org/10.1101/2020.03.02.968388
  8. ↑ Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Feb 19. pii: science.abb2507. doi: 10.1126/science.abb2507. PMID:32075877 doi:http://dx.doi.org/10.1126/science.abb2507

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