SARS-CoV-2 spike protein priming by furin

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Coronavirus (MERS). Transmission electron micrograph, artificially colored (cropped from NIAID public domain).

Many copies of the spike protein of the coronavirus that causes COVID-19 are seen, in the electron microscope, sticking out from the surface of the virion (virus particle), making it look somewhat like a crown -- hence the name coronavirus[1]. The spike protein is called protein S of the SARS-CoV-2 virus (see SARS-CoV-2 protein S). The spike protein plays a central role in binding to host cells, and getting the RNA genes of the virus into the cell, initiating infection. Thus, knowledge of its protein molecular structure and function is crucial to developing effective therapies and vaccines.

Movies for Slides

The movie at right (a multi-GIF, not interactive) can be dropped into a slide (Powerpoint, slides.google.com, libre office, etc.). It will animate when the slide is projected ("slide show" mode). As above: each chain of the homo-trimer is a different color; ACE2 binding site; furin cleavage site. To DOWNLOAD these files, right click, then save link as:

Please credit Proteopedia.Org in accord with our license, and Wrobel and coworkers[3] for their cryo-EM structures.

See Also

Methods

Structures Chosen

6ZGG and 6ZGI by Wrobel et al.[3] were chosen because they have substantially fewer missing amino acids than do the structures by Walls et al.[2] released several months earlier (6vxx and 6vyb). The two closed conformations determined by Wrobel et al.[3] (6zge and 6zgi) are nearly identical: RMSD for a structural alignment of 3,294 alpha carbons is 0.29 Å.

Alignment and Morphing

6ZGG (an open conformation) was aligned with 6ZGI (a closed conformation) using the Iterative Magic Fit of Swiss-PDB-Viewer. This aligned 1,828 alpha carbons (mainly the core of the structure, regions S2) with RMSD 1.34 Å. The closed model was morphed (linear interpolation) to the open model using the server provided by Karsten Theis, requesting 8 intermediate frames. The resulting 10-frame PDB file was loaded into the Jmol Java application. The alpha carbons were selected ("select *.ca") and written into a separate file, which was uploaded to Proteopedia for use in the above morph scenes: Image:Morf-6zgi-to-6zgg-alpha-carbons-only.pdb.

ACE2 Binding Site

6LZG is a 2.5 Å crystal structure of the receptor-binding domain of spike protein bound to ACE2. FirstGlance in Jmol reports that its Rfree is much better than average at this resolution. The Contacts and Non-Covalent Interactions tool in FirstGlance in Jmol identifies all the likely interactions between ACE2 and the spike protein. The interacting spike protein atoms are:

  • 1 salt bridge (Ly2417 to Asp30 in ACE2).
  • No cation-pi interactions.
  • 25 spike protein atoms are in putative hydrogen bonds with ACE2 atoms (oxygens or nitrogens within 3.5 Å of each other).
  • 6 spike protein atoms are water-bridged to ACE2 atoms.
  • 32 spike protein atoms are in putative van der Waals interactions with ACE2 atoms (carbons within 4.0 Å of each other).

18 spike protein amino acids are involved in these interactions. Their alpha carbons are selected by this Jmol command script:

select *.ca and (lys417,gly446,tyr449,leu455,phe456)
select selected or (*.ca and (ala475, glu484, phe486, asn487, tyr489))
select selected or (*.ca and (gln493, gly496, (gln498 and conformation=1), thr500, asn501))
select selected or (*.ca and (gly502, tyr505, gln506))
color magenta


References

  1. 1.0 1.1 1.2 1.3 Pillay TS. Gene of the month: the 2019-nCoV/SARS-CoV-2 novel coronavirus spike protein. J Clin Pathol. 2020 Jul;73(7):366-369. doi: 10.1136/jclinpath-2020-206658. Epub, 2020 May 6. PMID:32376714 doi:http://dx.doi.org/10.1136/jclinpath-2020-206658
  2. 2.0 2.1 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. 3.0 3.1 3.2 3.3 3.4 Wrobel AG, Benton DJ, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat Struct Mol Biol. 2020 Jul 9. pii: 10.1038/s41594-020-0468-7. doi:, 10.1038/s41594-020-0468-7. PMID:32647346 doi:http://dx.doi.org/10.1038/s41594-020-0468-7
  4. Thomas G. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat Rev Mol Cell Biol. 2002 Oct;3(10):753-66. doi: 10.1038/nrm934. PMID:12360192 doi:http://dx.doi.org/10.1038/nrm934
  5. Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, Lu G, Qiao C, Hu Y, Yuen KY, Wang Q, Zhou H, Yan J, Qi J. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell. 2020 Apr 7. pii: S0092-8674(20)30338-X. doi: 10.1016/j.cell.2020.03.045. PMID:32275855 doi:http://dx.doi.org/10.1016/j.cell.2020.03.045
  6. Fan X, Cao D, Kong L, Zhang X. Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein. Nat Commun. 2020 Jul 17;11(1):3618. doi: 10.1038/s41467-020-17371-6. PMID:32681106 doi:http://dx.doi.org/10.1038/s41467-020-17371-6
  7. Cai Y, Zhang J, Xiao T, Peng H, Sterling SM, Walsh RM Jr, Rawson S, Rits-Volloch S, Chen B. Distinct conformational states of SARS-CoV-2 spike protein. Science. 2020 Jul 21. pii: science.abd4251. doi: 10.1126/science.abd4251. PMID:32694201 doi:http://dx.doi.org/10.1126/science.abd4251

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