Coronaviruses have long infected humans, yet none caused the same devastation as SARS-CoV-2 has (Li et al., 2020; Huang et al., 2020). For instance, a virulent and lethal coronavirus, SARS-CoV-1, caused a much smaller outbreak in 2002–2003 (Lee et al., 2003; Peiris et al., 2003). Numerous human coronaviruses such as NL63-CoV cause common colds annually (Fouchier et al., 2004; van der Hoek et al., 2004). With an intermediate virulence, SARS-CoV-2 causes a fatality rate that is significantly lower than that of SARS-CoV-1, but much higher than that of NL63-CoV. Because of its intermediate virulence, SARS-CoV-2 carriers show clinical signs that facilitate the spread of the virus: they may develop mild or no symptoms, experience delayed onset of symptoms, develop low levels of neutralizing antibodies, or endure prolonged virus shedding period (Wu et al., 2020; Zhou et al., 2020; Wölfel et al., 2020; Gao et al., 2020; Kronbichler et al., 2020). These features contribute to the wide spread of SARS-CoV-2 and severe health outcomes, triggering a global COVID-19 pandemic that was unprecedented in the era of modern medicine. Understanding the molecular determinants of COVID-19 is crucial for comprehending the recent pandemic and preventing future ones.

SARS-CoV-2 spike protein played a central role in the COVID-19 pandemic. It guides viral entry into host cells and is also a major target for the host immune responses (Du et al., 2009; Li, 2016). On newly packaged virus particles, the trimeric spike protein has a pre-fusion structure in which three receptor-binding S1 subunits sit on top of a trimeric membrane-fusion S2 stalk (Figure 1A). During viral entry, a receptor-binding domain (RBD) in S1 binds to a receptor on host cell surface for viral attachment and S2 switches to a post-fusion structure for the fusion of viral and host membranes (Li, 2016; Li, 2015). SARS-CoV-2, SARS-CoV-1, and NL63-CoV can all use ACE2 as their receptor (Li et al., 2003; Li et al., 2005; Shang et al., 2020c; Wan et al., 2020a; Wu et al., 2009). Early in the pandemic, we described three distinct characteristics of SARS-CoV-2 spike: its exceptional binding affinity for human ACE2, its proteolytic activation by human protease furin, and its existence as a mixture of two conformations: an open conformation in which the RBD is exposed and accessible to ACE2 and a closed conformation in which the RBD is buried and inaccessible to ACE2 (Shang et al., 2020b). While much has been learned about the first two characteristics (Shang et al., 2020c; Lan et al., 2020; Essalmani et al., 2022; Peacock et al., 2021; Geng et al., 2022; Zhang et al., 2023), the third still remains poorly understood. Interestingly, SARS-CoV-1 spike is predominantly in the open conformation, whereas NL63-CoV spike remains closed (Walls et al., 2016; Wrobel et al., 2020; Gui et al., 2017). Thus, two key questions arise: what molecular switches regulate the conformation of coronavirus spikes and how do the conformational changes influence coronaviruses’ infectivity and host immune responses?

Figure 1

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In this study, we used cryo-EM and biochemical approaches to identify spike residue 417 as a molecular switch that regulates the conformation of SARS-CoV-2 spike. We delved deeper into how this molecular switch affects receptor binding, viral entry, and immune evasion by SARS-CoV-2. Through regulation of its spike’s conformations, SARS-CoV-2 may have struck a balance between infection potency and immune evasiveness.

To understand the molecular mechanism that controls the spike’s switching between open and closed conformations, we compared the sequences of SARS-CoV-2 and SARS-CoV-1 spikes in the context of their tertiary structures. We identified residue 417 as potentially a key difference between the two spikes: in the closed SARS-CoV-2 trimeric spike, Lys417 in the RBD from one spike subunit forms a hydrogen bond with the main chain of Asn370 in the RBD from another spike subunit, stabilizing the RBDs in the closed conformation (Walls et al., 2020; Figure 1B). In SARS-CoV-1 spike, however, this residue becomes a valine (Li et al., 2005; Shang et al., 2020a; Figure 1C), losing its capability to form the hydrogen bond with another spike subunit and potentially destabilizing the closed conformation of the spike. Thus, we hypothesized that a K417V mutation causes more SARS-CoV-2 spike molecules to take the open conformation. To test this hypothesis, we investigated the impact of the K417V mutation on the structure and function of SARS-CoV-2 spike using a combination of cryo-EM and biochemical approaches.

To examine how the K417V mutation affects the conformation of SARS-CoV-2 spike, we performed cryo-EM analysis of the RBD conformation of SARS-CoV-2 spike ectodomain containing either Lys417 or Val417. To this end, we introduced the K417V mutation into SARS-CoV-2 spike ectodomain and purified both versions of the protein: K417-spike containing Lys417 and V417-spike containing Val417. Due to the lack of the transmembrane anchor, the recombinant spike ectodomain was intrinsically unstable. To stabilize the recombinant spike ectodomain, we introduced six proline mutations into its S2 subunit to lock up its pre-fusion structure, introduced mutations to its furin motif to prevent it from being cleaved during molecular maturation, and added a C-terminal foldon tag to facilitate its trimerization (Shang et al., 2020b; Hsieh et al., 2020; Ye et al., 2022). We successfully obtained the stabilized K417-spike and V417-spike and collected cryo-EM data on both proteins (Figure 2—figure supplements 1 and 2; Supplementary file 1). For the K417-spike, 55% of the molecules were in the closed conformation with all three RBDs down, whereas the rest of the molecules (45%) were in the open conformation with one RBD up and two RBDs down (Figure 2A and B). In contrast, for the V417-spike, these numbers became 32 and 68% for the closed and open conformations, respectively (Figure 2C and D). Therefore, the K417V mutation allowed more SARS-CoV-2 spike molecules to take the open conformation, confirming our hypothesis.

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While the above cryo-EM approach examined the conformation of recombinant spike ectodomain, we further examined the impact of the K417V mutation on the membrane-anchored and full-length SARS-CoV-2 spike that do not contain S2 or furin motif mutations. It has been shown that ACE2 only binds to the standing-up RBD in the open spike (Gui et al., 2017; Ye et al., 2021), suggesting that the open spike conformation is necessary for ACE2 binding. Hence, we characterized the capabilities of K417-spike and V417-spike in binding ACE2. First, we expressed the K417-spike and V417-spike on human cell surface and performed a protein pull-down assay using recombinant human ACE2 as the bait and the cell-surface-anchored spikes as the target (Figure 3A). For cross-validation, both His-tagged ACE2 and Fc-tagged ACE2 were used. We previously showed that this pull-down assay is a reliable method to probe the RBD conformation of cell-surface-anchored spikes, with higher pull-down levels of spikes associated with more spike molecules in the open conformation (Shang et al., 2020b). Western blot analysis showed that some of the spike molecules had been cleaved at the S1/S2 boundary, confirming the intact furin motif (Figure 3A). The pull-down result showed that, compared to K417-spike, more V417-spike molecules had been pulled down by ACE2, suggesting that V417-spike had an increased probability of binding to ACE2 (Figure 3A). Second, we conducted a flow cytometry assay to detect the interactions between recombinant human ACE2 and cell-surface-anchored spikes (Figure 3B, Figure 3—figure supplement 1). Here, two versions of both K417-spike and V417-spike were used: one containing the intact furin motif and the other the inactivated furin motif. The result showed that V417-spike binds to ACE2 better than does K417-spike, no matter whether the furin motif was intact or inactivated (Figure 3B, Figure 3—figure supplement 1). Taken together, both protein pull-down and flow cytometry results reveal that the K417V mutation allowed more SARS-CoV-2 spike molecules to take the open conformation, confirming the cryo-EM data and our hypothesis.

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Numerical data for Figure 3B.

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Numerical data for Figure 3C.

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Raw image for Figure 3C.

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To understand the role of the spike’s conformations in viral entry, we conducted a pseudovirus entry assay. Specifically, retroviruses pseudotyped with SARS-CoV-2 spike (i.e., SARS-CoV-2 pseudoviruses) were evaluated for their capability to enter ACE2-expressing human cells. Two types of SARS-CoV-2 pseudoviruses were used: the K417-spike-charged pseudoviruses (i.e., K417-pseudoviruses) and V417-spike-charged pseudoviruses (V417-pseudoviruses). Both types of pseudoviruses contain the furin motif in their spike. Western blot analysis showed that some of the spike molecules had been cleaved at the S1/S2 boundary when expressed on pseudovirus surface, confirming the intact furin motif (Figure 3C). The pseudovirus entry result showed that V417-pseudoviruses entered cells more efficiently than did K417-pseudoviruses (Figure 3C). Thus, the open spike enhances not only ACE2 binding, but also viral entry.

To understand the role of the spike’s conformation in immune evasion, we analyzed how neutralizing antibodies recognize the RBD in the context of the trimeric spike protein. To this end, we summarized the binding sites of known neutralizing antibodies on the RBD (Figure 4A). These neutralizing antibodies were discovered individually from COVID-19 patients. They generally recognize five groups of neutralizing epitopes on the RBD (Starr et al., 2021; Dussupt et al., 2021; Scheid et al., 2021; Fedry et al., 2021). Three groups of these RBD epitopes are only accessible to neutralizing antibodies when the spike adopts the open conformation (Starr et al., 2021; Dussupt et al., 2021). In comparison, the other two groups of RBD epitopes are accessible to neutralizing antibodies when the spike adopts either open or closed conformation (Scheid et al., 2021; Fedry et al., 2021). In addition to the above conventional antibodies, neutralizing nanobodies (which are single-domain antibodies derived from camelid animals) have also been discovered to target the RBD. Because of their single-domain structure, nanobodies are known to bind to cryptic epitopes on viral targets. We recently discovered four RBD-targeting nanobodies, named Nanosota-1, -2, -3, and -4 (Ye et al., 2021; Ye et al., 2023; Figure 4B). Among them, Nanosota-2 binds to an epitope on the RBD that almost completely overlaps with the ACE2-binding site. Interestingly, the Nanosota-2 epitope is only accessible to Nanosota-2 when the RBD is in the open conformation (Ye et al., 2023). This result suggests that even with the small size of nanobodies, SARS-CoV-2 may be able to evade some of them when its spike is in the closed conformation. Overall, these epitope-based analyses reveal that SARS-CoV-2 spike in the closed conformation can evade significant amounts of neutralizing antibodies, confirming our previous hypothesis that the closed conformation of the spike is a viral strategy for immune evasion (Shang et al., 2020b).

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To further understand the role of the K417 mutation in ACE2 binding and viral entry, we examined how the K417 mutation directly affects the RBD’s binding affinity for ACE2 instead of the trimeric spike’s. The structure of SARS-CoV-2 RBD complexed with human ACE2 showed that Lys417 in SARS-CoV-2 RBD is directly involved in ACE2 binding by forming a salt bridge with Asp30 in human ACE2 (Lan et al., 2020; Figure 5A). In contrast, the corresponding residue in SARS-CoV-1 RBD is a valine that does not form any direct interactions with human ACE2 (Li et al., 2005; Figure 5B). Here, we introduced the K417V mutation to SARS-CoV-2 RBD and investigated the binding interactions between the recombinant SARS-CoV-2 RBD (containing either Lys417 or Val417) and cell-surface-anchored human ACE2 using flow cytometry. The result showed that the K417V mutation reduced the RBD’s binding affinity for ACE2 (Figure 5C, Figure 5—figure supplement 1). Thus, the K417V mutation has contrasting effects on the RBD and the trimeric spike in terms of ACE2 binding: it weakens the RBD’s ability to bind to ACE2 by eliminating a favorable interaction at the RBD/ACE2 interface, but it increases the trimeric spike’s probability of binding to ACE2 by enabling more spike molecules to assume the open conformation.

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Numerical data for Figure 5C.

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To summarize, we identified and investigated a molecular switch regulating the conformation of SARS-CoV-2 spike protein. We used multiple approaches: cryo-EM study of recombinant spike ectodomains, biochemical investigation of cell-surface-anchored full-length and wild-type spikes, spike-mediated pseudovirus entry, and structural analysis of neutralizing antibody/nanobody epitopes. To date, several other studies also investigated the conformation of SARS-CoV-2 spike using cryo-EM (Wrobel et al., 2020; Walls et al., 2020; Ke et al., 2020; Xiong et al., 2020; Cai et al., 2020; Benton et al., 2021), some of which gave different ratios of open and closed spikes probably due to differences in sample preparations and/or protein constructions. In this study, the two spike constructs only differ at residue 417 and the two spike samples were prepared using the same procedure. Importantly, our cryo-EM analysis is consistent with our extensive biochemical and functional approaches. These varied experimental methods complement one another, making this study one of the most thorough in examining the conformation of SARS-CoV-2 spike.

We previously described a unique feature of the prototypic SARS-CoV-2 spike protein: it is present as a mixture of open and closed conformations (Shang et al., 2020b). Building on this discovery, this study demonstrates that the conformation of SARS-CoV-2 spike is regulated, at least in part, by a structural switch. Additionally, this research sheds light on the roles of the conformational changes in the spike’s functions. These findings have implications for the structure, function, and evolution of coronavirus spikes, as well as for the present and potential future coronavirus infections.

How has SARS-CoV-2 spike evolved to reach a balance of open and closed conformations? Through comparative studies of SARS-CoV-2 and SARS-CoV-1 spikes, we identified a molecular switch, RBD residue 417, that regulates the conformational changes of SARS-CoV-2 spike. Lys417 in the closed SARS-CoV-2 spike forms a hydrogen bond with another spike subunit, stabilizing the closed spike. In contrast, Val417 in SARS-CoV-1 spike cannot form such a hydrogen bond with another spike subunit, unable to stabilize the closed spike. When we introduced the K417V mutation to SARS-CoV-2 spike, more spike molecules turned open. Interestingly, Lys417 in the RBD of SARS-CoV-2 spike also directly interacts with ACE2, and we showed that the K417V mutation reduced the RBD’s binding affinity for ACE2. Hence, the K417V mutation has opposing effects on the RBD and the spike for their binding to ACE2. The net outcomes of the K417 mutation are to enhance the spike’s overall binding to ACE2 and the spike’s capability to mediate viral entry.

Besides residue 417, there are likely other molecular factors that influence the opening and closing of SARS-CoV-2 spike. Studies have shown that N-linked glycans on the spike and fatty acids bound to the spike both play a role in regulating its conformation (Toelzer et al., 2020; Sztain et al., 2021). As for protein-based factors, a D614G mutation that emerged later in the pandemic caused SARS-CoV-2 spike to favor the open conformation (Yurkovetskiy et al., 2020; Ozono et al., 2021). Furthermore, our earlier research indicated that three lysine residues kept SARS-CoV-2 Omicron spike in the open conformation (Ye et al., 2022). It is worth noting that residue 417 itself has been a mutational hotspot in SARS-CoV-2 spike; in some pre-Omicron variants, it changed to either asparagine or threonine, and in most Omicron subvariants, it became asparagine (Figure 1C). Given that the side chains of Asn417 and Thr417 might be too short to form a direct interaction with another spike subunit, the mutations at residue 417 could have influenced the conformation of the spike in subsequent SARS-CoV-2 variants. Nevertheless, this study focuses on prototypic SARS-CoV-2, offering comprehensive structural, biochemical, and functional data that pinpoint residue 417 as a key determinant in regulating the conformation of the prototypic spike. The molecular switch at residue 417 could have been a factor in the onset of the COVID-19 pandemic, as discussed below.

How does the conformation of SARS-CoV-2 spike influence both viral entry and immune evasiveness? Our study shows that, compared to its closed form, the open spike is more effective at binding to ACE2 and facilitating viral entry. This could enhance SARS-CoV-2’s ability to infect and spread among humans. We also found that certain epitopes on the RBD are accessible only in the open spike, allowing them to be targeted by neutralizing conventional antibodies and even compact single-domain nanobodies. This suggests the virus can efficiently evade hosts' immune defenses. The virus' ability to switch between open and closed spike conformations may be key to its balance of infectiousness and evasion of immunity. This delicate balance might explain the often mild symptoms and subdued, delayed immune reactions observed in SARS-CoV-2 carriers. In comparison, SARS-CoV-1 spike predominantly assumes the open conformation (89% open and 11% closed) (Gui et al., 2017), potentially leading to more pronounced symptoms and quicker, stronger immune reactions in those infected. Conversely, NL63-CoV spike remains closed (100% closed) (Walls et al., 2016), possibly resulting in even milder symptoms and more muted immune responses. Therefore, SARS-CoV-2’s blend of infectiousness and evasive abilities, differing from both the highly pathogenic SARS-CoV-1 and the milder NL63-CoV, might be a factor in its widespread transmission.

To summarize, Lys417 in SARS-CoV-2 spike aids in keeping the spike closed, potentially hindering ACE2 binding and viral entry, but providing an edge in immune evasion. Simultaneously, Lys417’s direct interaction with human ACE2 boosts ACE2 binding and viral entry, counteracting the limitations of the closed spike. This interesting mechanism helps SARS-CoV-2 maintain a delicate balance between infectiousness and evading host immune response.

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 3 and 5. The atomic models and corresponding cryo-EM density maps have been deposited into the PDB and the Electron Microscopy Data Bank, respectively, with accession numbers PDB 8UUL and EMD-42589 (prototypic SARS-CoV-2 spike containing Lys417 in the closed conformation), PDB 8UUM and EMD-42590 (prototypic SARS-CoV-2 spike containing Lys417 in the open conformation), PDB 8UUN and EMD-42591 (prototypic SARS-CoV-2 spike containing Val417 in the closed conformation), and PDB 8UUO and EMD-42592 (prototypic SARS-CoV-2 spike containing Val417 in the open conformation).

1. 1. Li F

   (2023) RCSB Protein Data Bank

   ID 8UUL. Prototypic SARS-CoV-2 spike containing Lys417 in the closed conformation.

   https://www.rcsb.org/structure/8UUL
2. 1. Li F

   (2023) Electron Microscopy Data Bank

   ID EMD-42589. Prototypic SARS-CoV-2 spike containing Lys417 in the closed conformation.

   https://www.ebi.ac.uk/emdb/EMD-42589
3. 1. Li F

   (2023) RCSB Protein Data Bank

   ID 8UUM. Prototypic SARS-CoV-2 spike containing Lys417 in the open conformation.

   https://www.rcsb.org/structure/8UUM
4. 1. Li F

   (2023) Electron Microscopy Data Bank

   ID EMD-42590. Prototypic SARS-CoV-2 spike containing Lys417 in the open conformation.

   https://www.ebi.ac.uk/emdb/EMD-42590
5. 1. Li F

   (2023) RCSB Protein Data Bank

   ID 8UUN. Prototypic SARS-CoV-2 spike containing Val417 in the closed conformation.

   https://www.rcsb.org/structure/8UUN
6. 1. Li F

   (2023) Electron Microscopy Data Bank

   ID EMD-42591. Prototypic SARS-CoV-2 spike containing Val417 in the closed conformation.

   https://www.ebi.ac.uk/emdb/EMD-42591
7. 1. Li F

   (2023) RCSB Protein Data Bank

   ID 8UUO. Prototypic SARS-CoV-2 spike containing Val417 in the open conformation.

   https://www.rcsb.org/structure/8UUO
8. 1. Li F

   (2023) Electron Microscopy Data Bank

   ID EMD-42592. Prototypic SARS-CoV-2 spike containing Val417 in the open conformation.

   https://www.ebi.ac.uk/emdb/EMD-42592

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Decision letter after peer review:

Thank you for submitting your article "Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, including Lejla Zubcevic as Reviewing Editor and Reviewer #1, and the evaluation has been overseen by José Faraldo-Gómez as Senior Editor. The following individual involved in review of your submission has agreed to reveal their identity: Yi Ren (Reviewer #3).

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Essential revisions:

All reviewers agreed that this is a well-executed study with significant findings. However, we agreed that a few revisions should be made prior to publication. We have compiled the list of requests, comments, and questions below.

1. In order to be able to comment on the molecular mechanism of close-to-open transition, the authors need to look at atomic models of the RBD captured in both closed and open states. The reviewers would like the authors to submit an open RBD structure. The data for this should already exist (4.6A K417V/furin motif deletion mutant 3D reconstruction presented in figure 2C). To get an idea of the general mechanism of the closed-to-open transition, the authors could build a (where appropriate, side chain-less model) of the 4.6A K417V/furin motif deletion mutant, for which the data already exists.

2. We would encourage both a comparison with the FnM-deletion (100% closed) structure and an internal comparison between the open and closed protomers in the "open" structure to gain an insight into the mechanism.

3. The way it is explained in the methods, it would appear that only the highest resolution class is taken into consideration when the percentage occupancies are calculated for the open and closed states. We are not convinced that this is the most appropriate way to analyze the data because it is inherently biased towards more structurally stable classes. Other open conformations might exist at lower resolutions. Ideally, the state occupancy percentages should be based on the total particle count. For example, assuming that the open conformation is more unstable than the closed one, the real distribution could be 90% open and 10% closed, where only the 10% are selected and contribute to the high resolution reconstruction. In this case, it'd be wrong to say that 100% of the particles are in the closed conformation when the data actually says that 100% of the high resolution particles (and 10% of the total) are in the closed conformation. At the very least, the authors should discuss this aspect of data analysis and explain the implications for their hypothesis.

4. The authors should create a figure that explains their cryo-EM workflow for analysis in detail (representative micrograph, 2D classification, 3D classifications, etc). This figure should also contain local resolution plots and Euler angle distribution plots.

5. The PDB validation and visual inspection of maps indicates that lots of residues/regions do not fit the map very well. Lots of side chains were built with no density supporting them. We encourage the authors to go back to these models and a. remove segments of the model that are not supported by experimental density and b. re-build the backbone of the protein in parts of the protein where it does not fit the density well. This is particularly an issue because the authors discuss interaction networks in regions with poor density (Lys417 and it's interaction partner are part of this region too). As requested in point 4, a local resolution plot of the 3D model will also come in handy for the readers here to easily estimate the accuracy of the map in different regions of the protein.

6. The authors do not show a WT control in their mouse immunization experiments (figure 5). This control should be included.

7. The authors should comment on why we only observe one RBD in the up conformation, despite point mutations, especially Lys417Ala, being introduced to all 3 protomers? Are there factors that might be missing from the experimental system that might play a role in stabilizing the "fully open" i.e. all 3 RBDs in the up conformation.

8. Is there co-operativity in the trimer? E.g., does releasing one RBD change the open-to-closed equilibrium for the other two? And do the furin motif and the salt bridge act independently of each other?

9. The WT SARS-CoV-2 (containing the FnM) still performs better than the point mutant (FnM-point) in virus entry assays, suggesting that the charges within the FnM might play an important role. Have the authors created a SARS-CoV-2 with a GSGS-linker for comparison? And SARS-CoV-2 with the Arg replaced with Lys (which wouldn't be cleaved by furin)?

10. Is it accurate that the structure of RaTG13-CoV is always in the closed conformation or is this an artefact of experimental conditions? This structure was crosslinked, which could have led to a 100% closed population.

11. Is it known what allows the RaTG13 spike molecule to switch into an open conformation? Are charged residues expected at play in this scenario as well (i.e., does RaTG13 have a lysine residue in the same position as SARS-CoV-2)? For comparison purposes, it would be helpful to know what residue is at the Lys417-equivalent position in RaTG13.

12. How well does the WT SARS-CoV-1 spike construct (controlled for pre-fusion) bind ACE2 and behave in the pseudovirus entry experiment? Is it comparable to the SARS-CoV-2 K417V mutant? If it is, this would suggest that the two major switches for dictating the open/closed confirmations are predominantly due to the presence of the furin motif loop and the salt bridge. If not, this could point to other factors involved in contributing to the conformational differences between SARS-CoV-1 and -2.

13. Lys417 has been identified as important for ACE2 binding. Can the authors comment on this, in the light of this new data.

14. Glycans and fatty acids have also been suggested to play a role in the open-to-closed transition. Can the authors comment on their potential roles in the light of this new data.

15. The illustration of the mechanism of the closed-to-open transition Figure S3A was difficult to interpret. Similarly, the interfaces between S1 and NTD were also difficult to glean from the figure. We would encourage the authors to make two separate figures (or at least, two panels in one figure) to illustrate this better. Also, a surface representation might work better to show the interface between S1 and NTD.

16. Could the authors include more spike structures (i.e. closed form of D614G) for comparing the interfaces in Figure S3? Spike proteins features extensive conformational heterogeneity. Even within the same category of open or closed spike, further classification generates slightly different structures. It is not entirely clear what level of changes is significant.

17. Line 99-101: The authors should quote A. C. Walls et al., Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, (2020).

18. Line 136-137: Reference for the double proline/C-term foldon.

19. It would be helpful to include expected molecular masses in the legends of Figures 1C, 3B and 4B where expected bands should appear.

20. It would be very helpful to include a table of experimental outcomes that includes the protein conformations of all WT proteins (CoV-1, CoV-2, and RaTG13) and mutants, a summary of ACE2 binding and pseudovirus entry.

21. In line 441, is "26,126 particles" correct? This number seems to refer to particles selected from 2D for the entire dataset.

Reviewer #1 (Recommendations for the authors):

The conformation of the SARS-CoV-2 spike protein receptor binding domain (RBD) has implications for binding to the host cell surface receptor: the open conformation is required for binding, but it also makes the virus more likely to be detected by the host's immune system. SARS-CoV-2 spike protein RBD has been observed with equal probability in both open and closed conformations but the mechanism of the transition from the closed to the open state is not known.

Here, Wan et al. present data that suggests that the flexible linker between S1 and S2, which contains a furin binding motif, is an important factor in facilitating this transition.

Importantly, the authors' findings suggest that it is not the furin motif itself but the flexible linker that facilitates the transition to the open conformation.

The study stretches from basic biochemistry to structural biology to in vivo experiments. However, the work can be strengthened by some additional data, data analysis and improved presentation of the structural biology section. In addition, some clarification regarding the in vivo data is required.

The authors present an interesting hypothesis that by being equally able to occupy the open and closed RBD conformations, SARS-Cov-2 has evolved to have high viral potency as well as successfully evade the host immune response. This is an interesting insight into viral evolution which may lead to novel avenues for future research.

I have the following comments:

1. To be able to comment on the molecular mechanism of close-to-open transition, the authors need to look at atomic models of the RBD captured in both closed and open states. The reviewers would like the authors to submit an open RBD structure. The data for this should already exist (4.6A K417V/furin motif deletion mutant 3D reconstruction presented in figure 2C). To get an idea of the general mechanism of the closed-to-open transition, the authors could build a (where appropriate, side chain-less model) of the 4.6A K417V/furin motif deletion mutant, for which the data already exists.

2. The authors should compare the open RBD structure with the FnM-deletion (100% closed) structure. In addition, they should make an internal comparison between the open and closed protomers in the "open" structure to gain an insight into the mechanism.

3. The way it is explained in the methods, only the highest resolution class is taken into consideration when the percentage occupancies are calculated for the open and closed states. This approach is inherently biased towards more structurally stable classes. Other open conformations might exist at lower resolutions. Ideally, the state occupancy percentages should be based on the total particle count.

For example, assuming that the open conformation is more unstable than the closed one, the real distribution could be 90% open and 10% closed, where only the 10% are selected and contribute to the high-resolution reconstruction. In this case, it'd be wrong to say that 100% of the particles are in the closed conformation when the data actually says that 100% of the high-resolution particles (and 10% of the total) are in the closed conformation. At the very least, the authors should discuss this aspect of data analysis and explain the implications for their hypothesis.

4. The authors should create a figure that explains their cryo-EM workflow for analysis in detail (representative micrograph, 2D classification, 3D classifications, etc). This figure should also contain local resolution plots and Euler angle distribution plots.

5. The PDB validation and visual inspection of maps indicates that lots of residues/regions do not fit the map very well. Lots of side chains were built with no density supporting them. The authors should: a. remove segments of the model that are not supported by experimental density and b. re-build the backbone of the protein in parts of the protein where it does not fit the density well. This is particularly an issue because the authors discuss interaction networks in regions with poor density (Lys417 and its interaction partner are part of this region too).

6. The authors do not show a WT control in their mouse immunization experiments (figure 5). This control should be included.

7. The authors should discuss the Lys417 residue and its involvement in ACE2 binding.Reviewer #2 (Recommendations for the authors):

Wan et al., investigate some of the major structural differences between the SARS-CoV-1, SARS-CoV-2, and RaTG13-CoV spike proteins to better understand why SARS-CoV-2 led to a global pandemic in humans. In particular, the study focuses on the SARS-CoV-2 spike (S) protein in the pre-fusion conformation, used by the virus to bind and enter host cells. The pre-fusion conformation of the S protein is known to have either open, closed or a mixture of open/closed conformations within the receptor-binding domain (RBD), depending on the type of coronavirus. The SARS-CoV-2 RBD is found in both the open and closed conformations while SARS-CoV-1 and RaTG13-CoV are found in the open and closed, respectively. The authors investigate the contributions of two unique structural features of the SARS-CoV-2 S protein, a furin binding motif within a loop as well as a lysine residue (position 417), to understand the observed mixture of conformations. Using a combination of mutational analyses, biochemical assays, structural studies, and mouse models, the authors show that both structural motifs (the furin loop and lysine residue) contribute to the ability of the protein to switch between the open and closed conformations. Furthermore, this switching between conformations most likely contributes to the effectiveness of SARS-CoV-2 establishing widespread infections in humans. Overall, this very interesting study is well conducted and will aid in the development of additional SARS-CoV-2 studies, as well as inform how other coronaviruses may employ the same strategies.

Comments:

1) It would be important to know how well the WT SARS-CoV-1 spike construct (controlled for pre-fusion) binds ACE2 and behaves in the pseudovirus entry experiment. Is it comparable to the SARS-CoV-2 K417V mutant? If it is, this would suggest that the two major switches for dictating the open/closed confirmations are predominantly due to the presence of the furin motif loop and the salt bridge. If not, this could point to other factors involved in contributing to the conformational differences between SARS-CoV-1 and -2.Reviewer #3 (Recommendations for the authors):

In this work, the authors have aimed to identify molecular switches regulating the conformations of SARS-CoV-2 spike protein and to investigate their effects on the potency and immune evasiveness of SARS-CoV-2. The authors have identified two such molecular switches, the furin motif and the K417 residue at the interface of the RBD domains in closed spike. The strength of the work is the comprehensive approach (SARS-CoV-2/RaTG13-CoV engineering, ACE2 binding, cryo-EM, pseudovius entry assays, etc). The authors clearly demonstrate the effects of furin motif and K417 on the ratios of open and closed spikes, and consistently, on ACE2 binding and pseudovirus entry. The correlation between spike conformations and immune evasiveness is an intriguing observation, although it remains to be more vigorously tested in future studies.

[Editors’ note: further revisions were suggested prior to acceptance, as described below.]

Thank you for resubmitting your work entitled "Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein" for further consideration by eLife. Your revised article has been evaluated by Diane Harper (Senior Editor) and a Reviewing Editor.

The manuscript has been improved but there are some remaining issues that need to be addressed, as outlined below:

Reviewer #1 (Recommendations for the authors):

Here, Li et al. identify a molecular switch within the SARS-CoV-1/2 spike proteins, in position 417. Based on comparisons between CoV-1 and CoV-2 sequences, the authors propose that the nature of the residue of this position determines whether the spike favors a closed or an open conformation. The authors present cryo-EM and biochemical data in support of their hypothesis. The paper will be of general interest to those interested in molecular mechanisms of viral infection by SARS-CoV-2 and other coronaviruses.

The authors have submitted a streamlined and improved manuscript. I only have a few comments to add.

– My main concern is that the word "affinity" is not used properly in some parts of the paper. For example, in the abstract, the authors state "The net outcomes of this (K417V) mutation are to allow the spike to bind ACE2 more tightly…". This is not really what the data says- the mutation seems to increase the probability of "open" spike and therefore increases the probability of spike binding. In fact, the data shows that K417V binds less tightly to ACE2 than K417.

In lines 116-118 the authors write "It has been shown that ACE2 only binds to the standing-up RBD in the open spike (28, 33), suggesting that open spike binds to ACE2 with higher affinity than the closed spike." A more accurate statement would be that the open spike conformation is necessary for ACE2 binding.

This continues in lines 127-129 "The pull-down result showed that compared to K417-spike, more V417-spike molecules had been pulled down by ACE2, suggesting that V417-spike has a higher affinity for ACE2 (Figure 3A)." This experiment does not say anything about binding affinity, but it does suggest that the binding probability between the spike protein and ACE2 is increased in V417.

In the summary of findings in lines 184-187: "it weakens the RBD's ability to bind to ACE2 by eliminating a favorable interaction at the RBD/ACE2 interface, but it strengthens the trimeric spike's binding affinity for ACE2 by enabling more spike molecules to assume the open conformation." A more accurate statement would be that the V417 increases the probability of binding to ACE2 because it increases the probability of the open spike conformation.

Essential revisions:

All reviewers agreed that this is a well-executed study with significant findings. However, we agreed that a few revisions should be made prior to publication. We have compiled the list of requests, comments, and questions below.

1. In order to be able to comment on the molecular mechanism of close-to-open transition, the authors need to look at atomic models of the RBD captured in both closed and open states. The reviewers would like the authors to submit an open RBD structure. The data for this should already exist (4.6A K417V/furin motif deletion mutant 3D reconstruction presented in figure 2C). To get an idea of the general mechanism of the closed-to-open transition, the authors could build a (where appropriate, side chain-less model) of the 4.6A K417V/furin motif deletion mutant, for which the data already exists.

The revised manuscript centers on residue 417, which acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike. It has omitted the data and discussion about the furin motif deletion mutant (Figure 1). Accordingly, the title of the manuscript has been changed to “Lys417 acts as a molecular switch regulating the conformation of SARS-CoV-2 spike protein”.

In the revised manuscript, we have developed new stabilized versions of SARS-CoV-2 spike ectodomain. This was achieved by incorporating six proline mutations into the S2 subunit, an increase from the two proline mutations used in earlier versions. Subsequently, we acquired new cryo-EM data for these proteins at significantly improved resolutions and constructed new atomic models for each of the samples (Figure 2).

2. We would encourage both a comparison with the FnM-deletion (100% closed) structure and an internal comparison between the open and closed protomers in the "open" structure to gain an insight into the mechanism.

The revised manuscript centers on residue 417, which acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike. It has omitted the data and discussion about the furin motif deletion mutant (Figure 1). Accordingly, the title of the manuscript has been changed to “Lys417 acts as a molecular switch regulating the conformation of SARS-CoV-2 spike protein”.

3. The way it is explained in the methods, it would appear that only the highest resolution class is taken into consideration when the percentage occupancies are calculated for the open and closed states. We are not convinced that this is the most appropriate way to analyze the data because it is inherently biased towards more structurally stable classes. Other open conformations might exist at lower resolutions. Ideally, the state occupancy percentages should be based on the total particle count. For example, assuming that the open conformation is more unstable than the closed one, the real distribution could be 90% open and 10% closed, where only the 10% are selected and contribute to the high resolution reconstruction. In this case, it'd be wrong to say that 100% of the particles are in the closed conformation when the data actually says that 100% of the high resolution particles (and 10% of the total) are in the closed conformation. At the very least, the authors should discuss this aspect of data analysis and explain the implications for their hypothesis.

Please see Figure 2—figure supplement1, Figure 2—figure supplement2, and Supplementary File 1 for the updated cryo-EM procedures.

4. The authors should create a figure that explains their cryo-EM workflow for analysis in detail (representative micrograph, 2D classification, 3D classifications, etc). This figure should also contain local resolution plots and Euler angle distribution plots.

Please see Figure 2—figure supplement1 and Figure 2—figure supplement2 for the cryo-EM workflow.

5. The PDB validation and visual inspection of maps indicates that lots of residues/regions do not fit the map very well. Lots of side chains were built with no density supporting them. We encourage the authors to go back to these models and a. remove segments of the model that are not supported by experimental density and b. re-build the backbone of the protein in parts of the protein where it does not fit the density well. This is particularly an issue because the authors discuss interaction networks in regions with poor density (Lys417 and it's interaction partner are part of this region too). As requested in point 4, a local resolution plot of the 3D model will also come in handy for the readers here to easily estimate the accuracy of the map in different regions of the protein.

The cryo-EM densities and the corresponding atomic models presented in this revision represent a substantial improvement over our previous submission. For detailed comparisons and data, refer to Figure 2—figure supplement1, Figure 2—figure supplement2, and Supplementary File 1.

6. The authors do not show a WT control in their mouse immunization experiments (figure 5). This control should be included.

The revised manuscript no longer includes mouse immunization data. Instead, it presents findings that the closed spike can evade the binding of many neutralizing antibodies and nanobodies (Figure 4).

7. The authors should comment on why we only observe one RBD in the up conformation, despite point mutations, especially Lys417Ala, being introduced to all 3 protomers? Are there factors that might be missing from the experimental system that might play a role in stabilizing the "fully open" i.e. all 3 RBDs in the up conformation.

We have added the following comment to the revised manuscript:

“In this study, both of the open spikes have only one RBD standing up and two RBDs lying down. This finding aligns with the results of several other structural studies on SARS-CoV-2 spike (29, 40, 41). However, some other studies have reported instances of open SARS-CoV-2 spike with either two or three RBDs standing up (42, 45). The cause for this discrepancy is unclear, but could be due to different sample preparations and/or protein constructions.”

8. Is there co-operativity in the trimer? E.g., does releasing one RBD change the open-to-closed equilibrium for the other two? And do the furin motif and the salt bridge act independently of each other?

We don't have the answers to the first two questions, and we believe they fall outside the scope of our current study. Regarding the last question, we have excluded data and discussions about the furin deletion mutant spike from the revised manuscript. Instead, the focus has shifted to residue 417 in the revised manuscript, pinpointing it as an important determinant that regulates the conformation of SARS-CoV-2 spike.

9. The WT SARS-CoV-2 (containing the FnM) still performs better than the point mutant (FnM-point) in virus entry assays, suggesting that the charges within the FnM might play an important role. Have the authors created a SARS-CoV-2 with a GSGS-linker for comparison? And SARS-CoV-2 with the Arg replaced with Lys (which wouldn't be cleaved by furin)?

We have excluded data and discussions about the furin deletion mutant spike from the revised manuscript. Instead, the focus has shifted to residue 417 in the revised manuscript, pinpointing it as an important determinant that regulates the conformation of SARS-CoV-2 spike.

10. Is it accurate that the structure of RaTG13-CoV is always in the closed conformation or is this an artefact of experimental conditions? This structure was crosslinked, which could have led to a 100% closed population.

The revised manuscript no longer includes discussion regarding the RaTG13-CoV spike.

11. Is it known what allows the RaTG13 spike molecule to switch into an open conformation? Are charged residues expected at play in this scenario as well (i.e., does RaTG13 have a lysine residue in the same position as SARS-CoV-2)? For comparison purposes, it would be helpful to know what residue is at the Lys417-equivalent position in RaTG13.

The revised manuscript no longer includes discussion regarding the RaTG13-CoV spike.

12. How well does the WT SARS-CoV-1 spike construct (controlled for pre-fusion) bind ACE2 and behave in the pseudovirus entry experiment? Is it comparable to the SARS-CoV-2 K417V mutant? If it is, this would suggest that the two major switches for dictating the open/closed confirmations are predominantly due to the presence of the furin motif loop and the salt bridge. If not, this could point to other factors involved in contributing to the conformational differences between SARS-CoV-1 and -2.

In response to the first question, the functions of the SARS-CoV-1 and SARS-CoV-2 spikes were thoroughly compared in one of our earlier publications (PubMed ID 32376634). The present study is specifically concentrated on SARS-CoV-2 spike.

In the revised manuscript, we added the percentages of open and closed SARS-CoV-1 spike particles:

“SARS-CoV-1 spike predominantly assumes an open conformation (89% open and 11% closed) (28).”

We also noted that there may be other factors contributing to the conformations of coronavirus spikes:

“Besides residue 417, there are likely other molecular factors that influence the opening and closing of SARS-CoV-2 spike. Studies have shown that N-linked glycans on the spike and fatty acids bound to the spike both play a role in regulating its conformation (43, 44). As for protein-based factors, a D614G mutation that emerged later in the pandemic caused SARS-CoV-2 spike to favor the open conformation (45, 46). Furthermore, our earlier research indicated that three lysine residues kept SARS-CoV-2 Omicron spike in the open conformation (32).”

13. Lys417 has been identified as important for ACE2 binding. Can the authors comment on this, in the light of this new data.

The revised manuscript includes new data indicating that the K417V mutation decreases the direct binding of the RBD to human ACE2 (Figure 5). Thus, our study reveals that the K417V mutation has opposing effects on the spike’s function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2.

14. Glycans and fatty acids have also been suggested to play a role in the open-to-closed transition. Can the authors comment on their potential roles in the light of this new data.

We have added the following discussion to the revised manuscript:

“Besides residue 417, there are likely other molecular factors that influence the opening and closing of SARS-CoV-2 spike. Studies have shown that N-linked glycans on the spike and fatty acids bound to the spike both play a role in regulating its conformation (43, 44).”

15. The illustration of the mechanism of the closed-to-open transition Figure S3A was difficult to interpret. Similarly, the interfaces between S1 and NTD were also difficult to glean from the figure. We would encourage the authors to make two separate figures (or at least, two panels in one figure) to illustrate this better. Also, a surface representation might work better to show the interface between S1 and NTD.

The revised manuscript no longer includes the packing analysis of the interfaces. Due to the relative mobility of the RBDs, an accurate packing analysis would require cryo-EM data of even higher resolutions. Therefore, the revised manuscript concentrates on insights gleaned from the overall cryo-EM structures, which are supported by a variety of biochemical and functional data. Collectively, our results reveal that residue 471 is the key regulator of SARS-CoV-2 spike's conformation.

16. Could the authors include more spike structures (i.e. closed form of D614G) for comparing the interfaces in Figure S3? Spike proteins features extensive conformational heterogeneity. Even within the same category of open or closed spike, further classification generates slightly different structures. It is not entirely clear what level of changes is significant.

The revised manuscript no longer includes the packing analysis of the interfaces. Due to the relative mobility of the RBDs, an accurate packing analysis would require cryo-EM data of even higher resolutions. Therefore, the revised manuscript concentrates on insights gleaned from the overall cryo-EM structures, which are supported by a variety of biochemical and functional data. Collectively, our results reveal that residue 471 is the key regulator of SARS-CoV-2 spike's conformation.

17. Line 99-101: The authors should quote A. C. Walls et al., Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, (2020).

This citation has been added to the revised manuscript:

“We identified residue 417 as potentially a key difference between the two spikes: in the closed SARS-CoV-2 trimeric spike, Lys417 in the RBD from one spike subunit forms a hydrogen bond with the main chain of Asn370 in the RBD from another spike subunit, stabilizing the RBDs in the closed conformation (29) (Figure 1B).”

18. Line 136-137: Reference for the double proline/C-term foldon.

References have been added to the revised manuscript:

“To stabilize the recombinant spike ectodomain, we introduced six proline mutations into its S2 subunit to lock up its pre-fusion structure, introduced mutations to its furin motif to prevent it from being cleaved during molecular maturation, and added a C-terminal foldon tag to facilitate its trimerization (20, 31, 32).”

19. It would be helpful to include expected molecular masses in the legends of Figures 1C, 3B and 4B where expected bands should appear.

In the revised figure 2 legend, we added the following description:

“The expected molecular weights of SARS-CoV-2 spike monomer and S2 monomer are ~180 kDa and ~80 kDa, respectively.”

20. It would be very helpful to include a table of experimental outcomes that includes the protein conformations of all WT proteins (CoV-1, CoV-2, and RaTG13) and mutants, a summary of ACE2 binding and pseudovirus entry.

In the revised manuscript, we have omitted the supplementary table that cataloged the conformation of spikes from multiple coronaviruses, including RaTG13. We believe that such an extensive summary of the literature is more suited to a comprehensive review article. Instead, the revised manuscript narrows its comparison to SARS-CoV-2, SARS-CoV-1, and NL63-CoV, as all three of these viruses use ACE2 as their receptor but result in different patient symptoms. We have encapsulated the conformations of the other two spikes as follows:

“SARS-CoV-1 spike predominantly assumes the open conformation (89% open and 11% closed) (28).” “ NL63-CoV spike remains closed (100% closed) (26).”

We also note that:

“To date, several other studies also investigated the conformation of SARS-CoV-2 spike using cryo-EM (27, 29, 39-42), some of which gave different ratios of open and closed spikes probably due to differences in sample preparations and/or protein constructions. In this study, the two spike constructs only differ at residue 417 and the two spike samples were prepared using the same procedure. Importantly, our cryo-EM analysis is consistent with our extensive biochemical and functional approaches. These varied experimental methods complement one another, making this study one of the most thorough in examining the conformation of SARS-CoV-2 spike.”

21. In line 441, is "26,126 particles" correct? This number seems to refer to particles selected from 2D for the entire dataset.

Please see Figure 2—figure supplement1, Figure 2—figure supplement2, and Supplementary File 1 for the updated cryo-EM procedures.

Reviewer #1 (Recommendations for the authors):

1. To be able to comment on the molecular mechanism of close-to-open transition, the authors need to look at atomic models of the RBD captured in both closed and open states. The reviewers would like the authors to submit an open RBD structure. The data for this should already exist (4.6A K417V/furin motif deletion mutant 3D reconstruction presented in figure 2C). To get an idea of the general mechanism of the closed-to-open transition, the authors could build a (where appropriate, side chain-less model) of the 4.6A K417V/furin motif deletion mutant, for which the data already exists.

The revised manuscript centers on residue 417, which acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike. It has omitted the data and discussion about the furin motif deletion mutant (Figure 1). Accordingly, the title of the manuscript has been changed to “Lys417 acts as a molecular switch regulating the conformation of SARS-CoV-2 spike protein”.

2. The authors should compare the open RBD structure with the FnM-deletion (100% closed) structure. In addition, they should make an internal comparison between the open and closed protomers in the "open" structure to gain an insight into the mechanism.

The revised manuscript centers on residue 417, which acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike. It has omitted the data and discussion about the furin motif deletion mutant (Figure 1). Accordingly, the title of the manuscript has been changed to “Lys417 acts as a molecular switch regulating the conformation of SARS-CoV-2 spike protein”.

3. The way it is explained in the methods, only the highest resolution class is taken into consideration when the percentage occupancies are calculated for the open and closed states. This approach is inherently biased towards more structurally stable classes. Other open conformations might exist at lower resolutions. Ideally, the state occupancy percentages should be based on the total particle count.

For example, assuming that the open conformation is more unstable than the closed one, the real distribution could be 90% open and 10% closed, where only the 10% are selected and contribute to the high-resolution reconstruction. In this case, it'd be wrong to say that 100% of the particles are in the closed conformation when the data actually says that 100% of the high-resolution particles (and 10% of the total) are in the closed conformation. At the very least, the authors should discuss this aspect of data analysis and explain the implications for their hypothesis.

Please see Figure 2—figure supplement1, Figure 2—figure supplement2, and Supplementary File 1 for the updated cryo-EM procedures.

4. The authors should create a figure that explains their cryo-EM workflow for analysis in detail (representative micrograph, 2D classification, 3D classifications, etc). This figure should also contain local resolution plots and Euler angle distribution plots.

Please see Figure 2—figure supplement1 and Figure 2—figure supplement2 for the cryo-EM workflow.

5. The PDB validation and visual inspection of maps indicates that lots of residues/regions do not fit the map very well. Lots of side chains were built with no density supporting them. The authors should: a. remove segments of the model that are not supported by experimental density and b. re-build the backbone of the protein in parts of the protein where it does not fit the density well. This is particularly an issue because the authors discuss interaction networks in regions with poor density (Lys417 and its interaction partner are part of this region too).

The cryo-EM densities and the corresponding atomic models presented in this revision represent a substantial improvement over our previous submission. For detailed comparisons and data, refer to Figure 2—figure supplement1, Figure 2—figure supplement2, and Supplementary File 1.

6. The authors do not show a WT control in their mouse immunization experiments (figure 5). This control should be included.

The revised manuscript no longer includes mouse immunization data. Instead, it presents findings that the closed spike can evade the binding of many neutralizing antibodies and nanobodies (Figure 4).

7. The authors should discuss the Lys417 residue and its involvement in ACE2 binding.

The revised manuscript includes new data indicating that the K417V mutation decreases the direct binding of the RBD to human ACE2 (Figure 5). Thus, our study reveals that the K417V mutation has opposing effects on the spike’s function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2.

Reviewer #2 (Recommendations for the authors):

Comments:

1) It would be important to know how well the WT SARS-CoV-1 spike construct (controlled for pre-fusion) binds ACE2 and behaves in the pseudovirus entry experiment. Is it comparable to the SARS-CoV-2 K417V mutant? If it is, this would suggest that the two major switches for dictating the open/closed confirmations are predominantly due to the presence of the furin motif loop and the salt bridge. If not, this could point to other factors involved in contributing to the conformational differences between SARS-CoV-1 and -2.

This revised manuscript focuses on residue 417 of SARS-CoV-2 spike. The comparison between the functions of SARS-CoV-1 and SARS-CoV-2 spikes was described in detail in one of our earlier publications (PubMed ID 32376634).

[Editors’ note: what follows is the authors’ response to the second round of review.]

Reviewer #1 (Recommendations for the authors):

The authors have submitted a streamlined and improved manuscript. I only have a few comments to add.

– My main concern is that the word "affinity" is not used properly in some parts of the paper. For example, in the abstract, the authors state "The net outcomes of this (K417V) mutation are to allow the spike to bind ACE2 more tightly…". This is not really what the data says- the mutation seems to increase the probability of "open" spike and therefore increases the probability of spike binding. In fact, the data shows that K417V binds less tightly to ACE2 than K417.

In the revised manuscript, we have changed “allow the spike to bind ACE2 more tightly” to “allow the spike to bind ACE2 with higher probability”.

In lines 116-118 the authors write "It has been shown that ACE2 only binds to the standing-up RBD in the open spike (28, 33), suggesting that open spike binds to ACE2 with higher affinity than the closed spike." A more accurate statement would be that the open spike conformation is necessary for ACE2 binding.

In the revised manuscript, we have changed “suggesting that open spike binds to ACE2 with higher affinity than does the closed spike” to “suggesting that the open spike conformation is necessary for ACE2 binding.”

This continues in lines 127-129 "The pull-down result showed that compared to K417-spike, more V417-spike molecules had been pulled down by ACE2, suggesting that V417-spike has a higher affinity for ACE2 (Figure 3A)." This experiment does not say anything about binding affinity, but it does suggest that the binding probability between the spike protein and ACE2 is increased in V417.

In the revised manuscript, we have changed “suggesting that V417-spike has a higher affinity for ACE2” to “suggesting that V417-spike had an increased probability of binding to ACE2”.

In the summary of findings in lines 184-187: "it weakens the RBD's ability to bind to ACE2 by eliminating a favorable interaction at the RBD/ACE2 interface, but it strengthens the trimeric spike's binding affinity for ACE2 by enabling more spike molecules to assume the open conformation." A more accurate statement would be that the V417 increases the probability of binding to ACE2 because it increases the probability of the open spike conformation.

In the revised manuscript, we have changed “it strengthens the trimeric spike's binding affinity for ACE2” to “it increases the trimeric spike's probability of binding to ACE2”.

Author details

1. Qibin Geng

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Writing – review and editing

   Contributed equally with

   Yushun Wan

   Competing interests

   No competing interests declared

2. Yushun Wan

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Writing – review and editing

   Contributed equally with

   Qibin Geng

   Competing interests

   No competing interests declared

3. Fu-Chun Hsueh

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Data curation, Validation, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

4. Jian Shang

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

5. Gang Ye

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-6034-2174

6. Fan Bu

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Formal analysis, Validation, Visualization, Writing – review and editing

   Competing interests

   No competing interests declared

7. Morgan Herbst

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Data curation, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

8. Rowan Wilkens

   1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
   2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

   Contribution

   Data curation, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

9. Bin Liu

   Hormel Institute, University of Minnesota, Austin, United States

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Funding acquisition, Validation, Investigation, Visualization, Writing – review and editing

   For correspondence

   liu00794@umn.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-6581-780X

10. Fang Li

    1. Department of Pharmacology, University of Minnesota Medical School, Minneapolis, United States
    2. Center for Coronavirus Research, University of Minnesota, Minneapolis, United States

    Contribution

    Conceptualization, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Writing – original draft, Project administration, Writing – review and editing

    For correspondence

    lifang@umn.edu

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-1958-366X

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