SARS-CoV-2 spike protein fusion transformation

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The spike protein of SARS-CoV-2 plays a central role in coronavirus attachment to the ACE2 receptor on host cells, and in getting the RNA genome of the virus into the host cell via fusion of the virus and host cell membranes, initiating infection.

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image SARS-CoV-2 spike protein undergoes a dramatic conformational rearrangement () that plays a central role in fusing the coronavirus membrane with the host cell membrane[1]. Similar conformational transformations have been observed for the spike protein of SARS-CoV[2] and mouse hepatitis virus[3], among others. These rearrangements also have much in common with the membrane fusion mechansism of influenza hemagglutinin[4]. The molecular scenes in this article are based on the cryo-EM pre- and post-fusion structures of SARS-CoV-2 spike protein reported July, 2020, by Cai, Zhang and coworkers with the group of Bing Chen[1]. Click the green links below to change the molecular scene. Drag to rotate. Zoom the molecule with your mouse wheel, or Shift-Drag up/down. The is a homo-trimer, each chain having a mature length of 1,261 amino acids. This pre-fusion cryo-EM structure 6xr8 is complete except for 110 residues of the C-terminus (narrow end), comprising 48 residues of the stem (heptad repeat 2 domain), a 23-residue trans-membrane domain, and a 39 residue cytoplasmic domain. as in Cai, Zhang et al. [1] (lengths): 14-306 (293): N-terminal domain. 307-330 (24): Linker. 331-528 (198): Receptor binding domain, binds to angiotensin converting enzyme 2 (ACE2). 529-591 (63): CTD1 (C terminal region of S1 fragment after furin cleavage). 592-676 (85): CTD2 (C terminus of S1 fragment after furin cleavage). 677-688 (12): Pink balls mark the furin cleavage site PRRAR (missing in this model due to disorder). 689-816 (128): Linker 817-825 (9): Fusion peptide (FP). 826-834 (9): Fusion peptide proximal region (FPPR). 835-910 (76): Linker 911-985 (75): Heptad repeat 1 (HR1) 986-1035 (49): Central helix (CH) 1036-1068 (33): Connector domain (CD) 1069-1162 (93): Linker 1163-1273 (111): Missing in this model due to disorder. Stem, transmembrane domain, cytoplasmic domain. It will be easier to see the domains if you look at only one of the three chains:   A protease, typically furin, cuts the chains at the position marked with Pink balls, but the assembly, now six chains, remains intact. The cut may facilitate extending one receptor binding domain to engage the ACE2 receptor. The cut divides each chain of protein S into an N-terminal S1 receptor-binding fragment, and a C-terminal S2 fusion fragment[1]. , will later separate. Binding to ACE2 and a second proteolytic cut are believed to trigger release of S1, leaving S2[1].

See Also

Methods

The pre-fusion structure 6xr8 was morphed to the post-fusion structure 6xra by linear interpolation, requesting 14 intermediate frames (16 total), using the server provided by Karsten Theis. This produced an 11 MB file, which took 25 sec to load into JSmol. Each script took a minimum of 8 sec to complete. To reduce the bulk of this file and processing times for JSmol, the alpha carbons were extracted (along with the MODEL and ENDMDL records) by deleting all other lines in the PDB file^[5]

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4} 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
2. ↑ 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
3. ↑ Walls AC, Tortorici MA, Snijder J, Xiong X, Bosch BJ, Rey FA, Veesler D. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11157-11162. doi:, 10.1073/pnas.1708727114. Epub 2017 Oct 3. PMID:29073020 doi:http://dx.doi.org/10.1073/pnas.1708727114
4. ↑ Pabis A, Rawle RJ, Kasson PM. Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms. Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7200-7207. doi:, 10.1073/pnas.1914188117. Epub 2020 Mar 18. PMID:32188780 doi:http://dx.doi.org/10.1073/pnas.1914188117
5. ↑ BBEdit (barebones.com) has a regular expression "grep" mode that was used to delete unwanted lines. Deletion was done by find and replace with nothing. First, REMARK lines were deleted by finding ^REMARK.*\n, and similarly HETATM lines. Finally, non-CA ATOM lines were found with ^ATOM [ \d]\d\d\d\d [NCOS][ B-Z].*\n, leaving ATOM CA lines, MODEL and ENDMDL lines. This strategy was used after two other strategies failed. Selecting *.ca in the Jmol Java application and saving them produced a PDB file with numerous errors. I was unable to get regular expression alternation to work in either macOS Darwin sed, or GNU sed, thus unable to extract the desired 3 line types with "sed -n". I was also unable to get BBEdit to delete lines not containing a specified string, e.g. find (?!MODEL).