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Molecular Architecture of the SARS-CoV-2 Virus
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Abstract
SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.
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“Therefore, the S protein is considered the main antigen for vaccine design.228–230”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [228]
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“The trimeric S protein on the surface of SARS-CoV-2 plays a key role in mediating host cell invasion.”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [228]
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BackgroundControlling the SARS-CoV-2 spike glycoprotein conformation
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Self-citationVulnerabilities in coronavirus glycan shields despite extensive glycosylation
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“Upon activation, S follows a classic pathway among class-I fusion proteins (Rey and Lok, 2018): it undergoes dramatic structural rearrangements involving shedding its S1 subunit and inserting the fusion peptide (FP) into the target cell membrane (Cai et al., 2020).”
Structure and assembly of the Ebola virus nucleocapsid
Wan, W., Kolesnikova, L., Clarke, M., Koehler, A., Noda, T., Becker, S., & Briggs, J. A. G. (2017) · Nature · doi:10.1038/nature24490 · Cited by 211 · cited 2×
“The paraformaldehyde fixation was proven to have little impact on the structures at this resolution (25, 27).”
Chang, C., Hsu, Y.-L., Chang, Y., Chao, F.-A., Wu, M., Huang, Y., Hu, C., & Huang, T.-H. (2008) · Journal of Virology · doi:10.1128/jvi.02001-08 · Cited by 199 · cited 1×
“According to the previous Small-angle X-ray scattering (SAXS) (Chang et al., 2009) and cryo-EM (Gui et al.”
Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein
Fan, X., Cao, D., Kong, L., & Zhang, X. (2020) · Nature Communications · doi:10.1038/s41467-020-17371-6 · Cited by 195 · cited 2×
“Densities of five N-linked glycans (N1098, N1074, N1158, N1173 and N1194) are displayed on the spike (Figure 3D), reminiscent to the recombinant postfusion structures (Cai et al., 2020; Fan et al., 2020).”
BackgroundCastaño‐Díez, D., Kudryashev, M., & Stahlberg, H. (2016) · Journal of Structural Biology · doi:10.1016/j.jsb.2016.06.005 · Cited by 145 · cited 1×
“List of Supplementary Materials: Materials and Methods Figures S1-S5 Tables S1 References (41-58)”
BackgroundAcidic pH-Induced Conformations and LAMP1 Binding of the Lassa Virus Glycoprotein Spike
Li, S., Sun, Z., Pryce, R., Parsy, M.-L., Fehling, S. K., Schlie, K., Siebert, C. A., Garten, W., Bowden, T. A., Strecker, T., et al. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005418 · Cited by 127 · cited 7×
“The rotational freedom of spikes is allowed by its low population density, which is prominently distinct from other enveloped viruses possessing class I fusion proteins (Harris et al., 2006; Li et al., 2016; Liu et al., 2008).”
InfluentialSelf-citationSite-Specific Glycosylation of Virion-Derived HIV-1 Env Is Mimicked by a Soluble Trimeric Immunogen
Struwe, W. B., Chertova, E. N., Allen, J. D., Seabright, G. E., Watanabe, Y., Harvey, D. J., Medina-Ramírez, M., Roser, J. D., Smith, R., Westcott, D., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.07.080 · Cited by 125 · cited 4×
“Furthermore, the lower levels of oligomannose-type glycans compared to HIV and LASV are also consistent with lower glycan density (Watanabe et al., 2020b; Watanabe et al., 2018).”
InfluentialSelf-citationDifferential processing of HIV envelope glycans on the virus and soluble recombinant trimer
Cao, L., Pauthner, M. G., Andrabi, R., Rantalainen, K. I., Berndsen, Z. T., Diedrich, J. K., Menis, S., Sok, D., Bastidas, R. B., Park, S. K. R., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06121-4 · Cited by 123
Structure of the Lassa virus glycan shield provides a model for immunological resistance
Watanabe, Y., Raghwani, J., Allen, J. D., Seabright, G. E., Li, S., Moser, F. A., Huiskonen, J. T., Strecker, T., Bowden, T. A., & Crispin, M. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803990115 · Cited by 113 · cited 1×
“Furthermore, the lower levels of oligomannose-type glycans compared to HIV and LASV are also consistent with lower glycan density (Watanabe et al., 2020b; Watanabe et al., 2018).”
BackgroundSelf-citationRitchie, G. E., Harvey, D. J., Feldmann, F., Ströeher, U., Feldmann, H., Royle, L., Dwek, R. A., & Rudd, P. M. (2010) · Virology · doi:10.1016/j.virol.2009.12.020 · Cited by 110 · cited 2×
“Overall, the presence of substantial complex-type glycosylation suggests that the budding route of SARS-CoV-2 into the lumen of endoplasmic reticulum-Golgi apparatus intermediate compartments (ERGICs) is not an impediment to glycan maturation and is consistent with analysis of SARS-CoV glycans (Ritchie et al., 2010) a…”
Kirchdoerfer, R. N., Wang, N., Pallesen, J., Wrapp, D., Turner, H. L., Cottrell, C. A., Corbett, K. S., Graham, B. S., McLellan, J. S., & Ward, A. B. (2018) · Scientific Reports · doi:10.1038/s41598-018-36918-8 · Cited by 98 · cited 1×
“The activation of S requires cleavage of S1/S2 by furin-like protease and undergoes the conformational change from prefusion to postfusion (Belouzard et al., 2009; Kirchdoerfer et al., 2018; Simmons et al., 2004; Simmons et al., 2013; Song et al., 2018).”
Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike ProteinPreprint
Casalino, L., Gaieb, Z., Goldsmith, J. A., Hjorth, C. K., Dommer, A. C., Harbison, A. M., Fogarty, C. A., de Barros, E. P., Taylor, B. C., McLellan, J. S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.11.146522 · Cited by 92
Structural and functional analysis of a potent sarbecovirus neutralizing antibody
Pinto, D., Park, Y., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., Marco, A. D., et al. (2020) · Worldwide Protein Data Bank · doi:10.2210/pdb6ws6/pdb · Cited by 82
Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane
Jin, J., Galaz-Montoya, J. G., Sherman, M. B., Sun, S., Goldsmith, C. S., O'Toole, E. T., Ackerman, L. D., Carlson, L. A., Weaver, S. C., Chiu, W., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.07.018 · Cited by 77 · cited 2×
“Its shape is in good comparison to a recently reported SARS-CoV-2 RNP conformation (Klein et al., 2020), as well as the in situ conformation of the chikungunya viral RNP, which is also positive stranded (Jin et al., 2018), but different from the MHV RNP released using detergent (Gui et al., 2017).”
Electron microscopy studies of the coronavirus ribonucleoprotein complex
Gui, M., Liu, X., Guo, D., Zhang, Z., Yin, C.-C., Chen, Y. Z., & Xiang, Y. (2017) · Protein & Cell · doi:10.1007/s13238-016-0352-8 · Cited by 75 · cited 2×
“, 2018), but different from the MHV RNP released using detergent (Gui et al., 2017).”
Self-citationViral Architecture of SARS-CoV-2 with Post-Fusion Spike Revealed by Cryo-EMPreprint
Liu, C., Yang, Y., Gao, Y., Shen, C., Ju, B., Liu, C., Tang, X., Wei, J., Ma, X., Liu, W., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.02.972927 · Cited by 59 · cited 2×
“S from the cell surface; 3) sample preparation procedure, as cryo-EM images of ßpropiolactone fixed viruses showed most spikes present on the virus are postfusion-like (Liu et al., 2020; Gao et al., 2020).”
Self-citationHuiskonen, J. T., Parsy, M.-L., Li, S., Bitto, D., Renner, M., & Bowden, T. A. (2014) · Journal of Visualized Experiments · doi:10.3791/51714 · Cited by 21 · cited 1×
“Assembly structure reconstruction Three representative SARS-CoV-2 virus (Figures 1B and 4D) and a bundle of postfusion S (Figure 3B) were reconstructed by projecting all spikes and RNPs onto their refined coordinates andmerging the structures using Jsubtomo (Huiskonen et al., 2014).”
Self-citationCoronavirus-like particles present in simian faeces
Caul, E. O., & Egglestone, S. (1979) · Veterinary Record · doi:10.1136/vr.104.8.168 · Cited by 19 · cited 2×
“Interestingly, an early observation of the MHV RNPs showed 15-nm-diameter helices with five subunits per turn (Caul and Egglestone, 1979).”
Purification and Electron Cryomicroscopy of Coronavirus Particles
Neuman, B. W., Adair, B. D., Yeager, M., & Buchmeier, M. J. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-181-9_12 · Cited by 12
Huiskonen, J. T., Parsy, M.-L., Li, S., Bitto, D., Renner, M., & Bowden, T. A. (2014) · Journal of Visualized Experiments · doi:10.3791/51714-v · Cited by 2
Self-citation
Flagged first, then by citations
6 of the 82 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Yao, 2020, Patient-derived mutations impact pathogenicity of SARS-CoV-2, medRxiv
Cited by
Sorted by citations
Mechanisms of SARS-CoV-2 entry into cells
Jackson, C. B., Farzan, M., Chen, B., & Choe, H. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00418-x · Cited by 3,022
Evolution of antibody immunity to SARS-CoV-2
Gaebler, C., Wang, Z., Lorenzi, J. C. C., Muecksch, F., Finkin, S., Tokuyama, M., Cho, A., Jankovic, M., Schaefer-Babajew, D., Oliveira, T. Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03207-w · Cited by 1,674
COVID-19 and the human innate immune system
Schultze, J. L., & Aschenbrenner, A. C. (2021) · Cell · doi:10.1016/j.cell.2021.02.029 · Cited by 714
“, 2020), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Kim et al., 2020; Wu et al., 2020; Yao et al., 2020; Zhang and Holmes, 2020) is a rather heterogeneous disease.”
BackgroundSARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography
Klein, S., Cortese, M., Winter, S. L., Wachsmuth-Melm, M., Neufeldt, C. J., Cerikan, B., Stanifer, M. L., Boulant, S., Bartenschlager, R. F. W., & Chlanda, P. (2020) · Nature Communications · doi:10.1038/s41467-020-19619-7 · Cited by 735
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
Turoňová, B., Sikora, M., Schürmann, C., Hagen, W. J. H., Welsch, S., Blanc, F. E. C., von Bülow, S., Gecht, M., Bagola, K., Hörner, C., et al. (2020) · Science · doi:10.1126/science.abd5223 · Cited by 641
Metadata
- Authors
- Yao, H., Song, Y., Chen, Y., Wu, N., Xu, J., Sun, C., Zhang, J., Weng, T., Zhang, Z., Wu, Z., Cheng, L., Shi, D., Lu, X., Lei, J., Crispin, M., Shi, Y., Li, L., & Li, S.
- Affiliations
- First Affiliated Hospital Zhejiang University (CN)
- Tsinghua University (CN)
- Center for Life Sciences (CN)
- University of Southampton (GB)
- Westlake University (CN)
- Corresponding author
- Li, Lanjuan
- Li, Sai
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-10
- Volume
- 183
- Issue
- 3
- Pages
- 730-738.e13
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7474903
- OpenAlex
- W3083130172
- Cited by
- 1,060
- References
- 82
- Citations by year
- 2026: 78 · 2025: 98 · 2024: 157 · 2023: 201 · 2022: 236 · 2021: 252 · 2020: 38
- FWCI
- 23.88
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- SSRN Electronic Journal (acceptedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- Funders
- Zhejiang University
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- SARS-CoV-2, spike protein, N-glycans, ribonucleoprotein, viral RNA packaging, viral assembly
- MeSH terms
- Betacoronavirus, SARS-CoV-2, Animals, Chlorocebus aethiops, Humans, Models, Molecular, Protein Conformation, Mass Spectrometry, Vero Cells, Viral Proteins, Virus Cultivation, Virus Assembly, Cryoelectron Microscopy
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