SARS-CoV-2 protein S

Function

The homotrimeric spike glycoprotein on the SARS-CoV2 virus envelope mediates the entry into the host cell. Every monomer consists of the two subunits S1 and S2. The SARS-CoV-2 spike S1 subunit binds the cellular receptor called angiotensin converting enzyme 2 (ACE2). This Binding triggers a cascade of events leading to the fusion of cell and virus membrane. After the prefusion trimer is destabilized, the S1 subunit is shedded leading to transition of the S2 subunit to a stable postfusion conformation. To engage a host cell receptor, the receptor-binding domain (RBD) of S1 undergoes hinge-like conformational rearrangement that transiently hides or exposes the residues necessary for receptor binding. ^[1] This "priming" step, triggered by proteases such as furin, is animated in a morph at SARS-CoV-2 protein S priming by furin.

Structure Description

Spike subunits S1 and S2 can be divided into several subdomains. The S1 subunit comprises a signal sequence (SS) on the N-terminal end, followed by a N-terminal domain (NTD) and the receptor binding domain (RBD). After two small subdomains (SD1/2), we find two protease cleavage sites (S1/S2 and S2’).The S2 subunit is composed of a fusion peptide (FP), two heptad repeats (HR1 and 2), a central helix (CH), a connector domain (CD), a transmembrane domain (TM) and the cytoplasmic tail (CT). ^[1]

The structure of the receptor binding domain (RBD) in complex with the human ACE2 receptor shows that interaction happens via the spike protein RBD and the ACE2 N-terminal peptidase domain. The RBD consists of a twisted five stranded antiparallel β-sheet (β1, β2, β3, β4 und β7) forming the core together with short connecting helices and loops. The spike receptor binding motif (RBM), containing most of the ACE2 contacting residues, is located as an extended insertion between the β4 and β7 strands consisting of short β-sheets (β5 and β6), α-helices (α4 and α5) and loops. The ACE2 N-terminal peptidase domain has two lobes that form the substrate binding site. The contact between RBM and ACE2 is made at the bottom side of the ACE2 small lobe, with a concave outer surface in the RBM accommodating the N-terminal helix of the ACE2 and thus generating an interface of 1687 Å^2. This interface contains a network of different interactions, including hydrophilic interactions with 13 hydrogen bonds and 2 salt bridges. Key residues for for receptor binding include the amino acids Leu544, Phe486, Gln493, and Asn 501. Leu 544 interacts with ACE2 residues Asp30, Lys31 and His34. Phe486, interacts with ACE2 GLN24, Leu79, Met82 (by van der Waals forces) and Tyr 83. Gln 493 forms a hydrogen bond with ACE2 Glu35 and interacts with Lys31 and His34. Another Hydrogen bond is formed between ACE2 Tyr 41 and Asn501 of one α-helix of the RBM. Further, Asn501 also interacts with the amino acid residues Lys353, Gly354 and Asp355. Outside the RBM, there is another unique ACE2-interacting residue Lys417, forming a salt bridge with ACE2 Asp30. ^{[2] [3]}

Fusion and Entry Mechanism

The task of the spike protein is to initiate the fusion and consequently, entry into the host cell. A key role in mediating these processes are the domains S-HR1 and S-HR2. The exact mechanism of entry and fusion of SARS-CoV-2 with/ into the host cell is still not fully known but it could be possible that the 2019-nCoV may have similar membrane fusion mechanism as that of SARS-CoV. The putative antiviral mechanism is that, after binding of RBD S1 subunit of 2019-nCoV spike protein to the receptor ACE2 on the host cell, S2 subunit changes conformation by inserting FP into the cell membranes, triggering the association between the HR1 and HR2 domains to form a six-helix-bundle, which brings the viral and cellular membranes in close proximity for fusion.^[4]

The spike protein fusion transformation is animated at SARS-CoV-2 spike protein fusion transformation, where the membrane fusion hypothesis is illustrated and explained.

Glycosylation of the Spike Protein

Coronavirus spike proteins are densely decorated by heterogenous N-linked glycans protruding from the trimer surface. SARS-CoV-2 S comprises 22 N-linked glycosylation sequons per protomer. N-linked glycans play a key role in proper protein folding and in priming by host proteases ^[5] Since glycans can shield the amino acid residues and other epitopes from cells and antibody recognition, glycosylation can enable the coronavirus to evade both the innate and adaptive immune responses. ^{[2] [6]}

Binding to human ACE2 and CLEC4M/DC-SIGNR receptors

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

Spike protein S1 (residue 14-685): attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 and CLEC4M/DC-SIGNR receptors and internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes. Spike protein S2 (residue 686-1273): mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Spike protein S2' (residue 816-1273): acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.^[7][8]

See Also

• Spike protein
  
• SARS-CoV-2 protein S priming by furin where the priming step induced by furin cleavage is animated.
  
• Coronavirus Disease 2019 (COVID-19)
  
• SARS-CoV-2_virus_proteins
  
• COVID-19 AlphaFold2 Models
  
• Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up about 6vsb

References

1. ↑ ^{1.0 1.1} Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S.; Goldsmith, Jory A.; Hsieh, Ching-Lin; Abiona, Olubukola et al. (2020): Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. In: Science 367 (6483), S. 1260–1263. DOI: 10.1126/science.abb2507.
2. ↑ ^{2.0 2.1} Lan, Jun; Ge, Jiwan; Yu, Jinfang; Shan, Sisi; Zhou, Huan; Fan, Shilong et al. (2020): Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. In: Nature. DOI: 10.1038/s41586-020-2180-5.
3. ↑ Yan, Renhong; Zhang, Yuanyuan; Li, Yaning; Xia, Lu; Guo, Yingying; Zhou, Qiang (2020): Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. In: Science 367 (6485), S. 1444–1448. DOI: 10.1126/science.abb2762.
4. ↑ Xia, Shuai; Zhu, Yun; Liu, Meiqin; Lan, Qiaoshuai; Xu, Wei; Wu, Yanling et al. (2020): Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. In: Cellular & molecular immunology. DOI: 10.1038/s41423-020-0374-2.
5. ↑ Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra; Wall, Abigail; McGuire, Andrew T.; Veesler, David (2020): Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. In: Cell. DOI: 10.1016/j.cell.2020.02.058.
6. ↑ Shen, Shuo; Tan, Timothy H. P.; Tan, Yee-Joo (2007): Expression, glycosylation, and modification of the spike (S) glycoprotein of SARS CoV. In: Methods in molecular biology (Clifton, N.J.) 379, S. 127–135. DOI: 10.1007/978-1-59745-393-6_9.
7. ↑ Modeling of the SARS-COV-2 Genome
8. ↑ Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J Proteome Res. 2020 Apr 3;19(4):1351-1360. doi: 10.1021/acs.jproteome.0c00129., Epub 2020 Mar 24. PMID:32200634 doi:http://dx.doi.org/10.1021/acs.jproteome.0c00129