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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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“In our experiments, we selected a BCoV as a model virus for SARS-CoV-2 to better match the morphology and shape of SARS-CoV-2) as well as for its biosafety level (BSL2) requirement (Abdelrahman et al. 2020; Cantu et al. 2023; Echchgadda et al. 2023; Vlasova et al. 2021; Yao et al. 2020; Clark 1993).”
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“Viral particles are ~100 nm in diameter and canonically composed of the spike (S), envelope (E), membrane (M), and nucleocapsid (N) [7,8] viral proteins.”
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Volkhina, I. V., & Butolin, E. G. (2022) · Biomeditsinskaya Khimiya · doi:10.18097/pbmc20226801007 · Cited by 5
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Integrin β3 N125 glycosylation is essential for human cytomegalovirus entry into fibroblasts
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“Modification can decrease the amount of BDNF available at synapses, ultimately weakening mechanisms of synaptic plasticity and neuronal adaptability (Yao et al., 2020).”
Su, J.-Y., Huang, X.-Q., Xu, H.-L., Zhou, J., & Meng, Z. (2022) · Journal of the Optical Society of America B · doi:10.1364/josab.470215 · Cited by 4
Chung, C. W., Irudayaraj, P., Lallow, E. O., Xu, Z., Park, Y. K., Kudchodkar, S. B., Montaner, L. J., Srinivasan, A., & Muthumani, K. (2024) · Frontiers in Virology · doi:10.3389/fviro.2024.1399993 · Cited by 5
G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication
Sekine, R., Takeda, K., Suenaga, T., Tsuno, S., Kaiya, T., Kiso, M., Yamayoshi, S., Takaku, Y., Ohno, S., Yamaguchi, Y., et al. (2025) · Communications Biology · doi:10.1038/s42003-024-07351-7 · Cited by 4
“The architecture of the SARS-CoV-2 RNA – NP ultrastructure is likely based on protein – protein interaction and the interaction of the NP and vRNA 26 .”
Structural glycobiology – from enzymes to organelles
Mycroft‐West, C. J., Leanca, M. A., & Wu, L. (2025) · Biochemical Society Transactions · doi:10.1042/bst20241119 · Cited by 4
PBS-DLS: A Novel Ultrasensitive Dynamic Light Scattering Immunoassay
Fang, H., Gong, T., Su, Y., Xiong, S., Yao, M., Guo, Q., Tong, W., Gan, T., Zhang, P., Liu, Q., et al. (2025) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.5c03548 · Cited by 4
Cryo-EM to visualize the structural organization of viruses
de Oliveira, G. A. P., & Silva, J. L. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.04.011 · Cited by 6
Stem cell-based therapy for COVID-19
Chen, X., Liu, B., Li, C., Wang, Y., Geng, S., Du, X., Weng, J., & Lai, P. (2023) · International Immunopharmacology · doi:10.1016/j.intimp.2023.110890 · Cited by 4
Chen, R., Fulton, K. M., Tran, A., Duque, D., Kovalchik, K. A., Caron, É., Twine, S. M., & Li, J. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100645 · Cited by 4
Zhang, Q., Yang, Y., Lan, J., Wang, Z., Gao, Y., Li, X., Mao, W., Xie, J., Mi, L.-Z., Zhang, X., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1259386 · Cited by 4
“Results showed that the maximum neutralizing ability of gsRBD-immunized sera against the Omicron (BQ.1.1) pseudovirus decreased by 40%-60% compared to the Omicron (B.1.1.529) strain (Supplementary Figures 7F, 8).”
BackgroundResultInfluentialSberna, G., Mija, C., Lalle, E., Rozera, G., Matusali, G., Carletti, F., Girardi, E., & Maggi, F. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25116156 · Cited by 4
“…3 and 4 showed a mean viral load of 1.4 Log copies/mL via a ddPCR. SARS-CoV-2, a highly infectious virus responsible for the COVID-19 pandemic [26 underscores the need for rapid methods to assess the risk of SARS-CoV-2 infection without When treated with PMAxx, the viral load decreased by a…”
MethodInfluentialOptical detection of infectious SARS-CoV-2 virions by counting spikes
Kudryavtsev, D. S., Mozhaeva, V. A., Ivanov, I. A., Siniavin, A. E., Kalmykov, A. S., Gritchenko, A. S., Khlebtsov, B. N., Wang, S., Kang, B., Tsetlin, V. I., et al. (2024) · Nanoscale · doi:10.1039/d4nr01236d · Cited by 4
Application of advanced bioimaging technologies in viral infections
Sun, Y., Cao, C., Peng, Y., Dai, X., Li, X., Li, J., Liang, T., Song, P., Ye, Y., Yang, J., et al. (2024) · Materials Today Physics · doi:10.1016/j.mtphys.2024.101488 · Cited by 4
Zhang, T., Yang, D., Tang, L., & Hu, Y. (2024) · Molecular Medicine Reports · doi:10.3892/mmr.2024.13272 · Cited by 5
Jhanwar, A., Sharma, D., & Das, U. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.134850 · Cited by 4
Smith, M. M., & Melrose, J. (2024) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.70033 · Cited by 4
“70 The SARS- CoV-2 virion is an enveloped particle with a diameter of around 60–100 nm. 71 ACE2 is accepted as the main host cell receptor on host cells.”
Bae, J., Bednář, P., Zhu, R., Bong, C., Bak, M. S., Stainer, S., Kim, K., Lee, J.-H., Yoon, C., Lee, Y., et al. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c11057 · Cited by 4
“32 We assume that the ozone-induced damage can decrease the Young’s modulus of the outer layer, leading to swelling of the virus particles.”
Targeting viral suppressor of RNAi confers anti-coronaviral activity
Chen, J., Mu, J., Zhou, K., Zhang, Y., Zhang, J., Shu, T., Shang, W., Ren, Y., Xu, X.-Q., Zhang, L., et al. (2024) · Molecular Therapy · doi:10.1016/j.ymthe.2024.12.009 · Cited by 4
Self-citationStructural biology of SARS-CoV-2 nucleocapsid
Kippes, O., Thorn, A., & Santoni, G. (2022) · Crystallography Reviews · doi:10.1080/0889311x.2022.2072835 · Cited by 4
“These may act with the RNA in a ‘beads on a string’ (see Figure 3(B)) stoichiometry [37].”
BackgroundCan plant-derived anti-HIV compounds be used in COVID-19 cases?
Das, D., Jena, A. B., Banerjee, A., Radhakrishnan, A., Duttaroy, A. K., & Pathak, S. (2022) · Medical Hypotheses · doi:10.1016/j.mehy.2022.110926 · Cited by 4
“Coronavirus strains A2A and A3I make up the majority of infections in Indian patients.”
InfluentialDisinfection Effect of Hexadecyl Pyridinium Chloride on SARS-CoV-2 in vitro
Chen, K., Ma, F., Wang, Q.-J., Wang, Y., Zhuang, X., Zhang, X.-N., Mao, H., & Zhang, Y. (2022) · Intervirology · doi:10.1159/000526241 · Cited by 4
“Yao et al. [9] reported the first full three-dimensional fine structure of SARS-CoV-2, while Zhou et al. [7] re-ported the full-length genome of 2019-nCoV.”
BackgroundCoronavirus peplomer interaction
Pak, M. C., Chakraborty, R., Kanso, M. A., Tontiwattanakul, K., Kim, K.-I., & Giacomin, A. J. (2022) · Physics of Fluids · doi:10.1063/5.0120167 · Cited by 4
Structural characteristics of the SARS-CoV-2 Omicron lineages BA.1 and BA.2 virions
Ma, X., Wang, Y., Gao, Y., Wang, Y., Yan, A., Chen, J., Zhang, L., Wang, P., Zhao, J., & Liu, Z. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01385-9 · Cited by 4
“In contrast, the wild type (WT) SARSCoV-2 virions are oblate spheroidal.(1) The mean diameter of Omicron BA.”
BackgroundMethodResultACE2 Receptor: A Potential Pharmacological Target in COVID-19
Zhu, Y., Zhang, S., Wang, Z., Wang, Z., & Zhu, S. (2023) · Current Protein and Peptide Science · doi:10.2174/1389203724666230816092518 · Cited by 4
Condensates of SARS-CoV-2 Nucleoprotein on Viral RNA and Their Small Molecule Modulators (A Review)
Svetlova, Y. I., Pavlova, I., Aralov, A. V., & Varizhuk, A. M. (2023) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162023050229 · Cited by 4
Human ACE2 protein is a molecular switch controlling the mode of SARS-CoV-2 transmission
Yang, C. S., Liao, C., Hsu, H.-W., Liang, J., Chang, C.-S., Ko, H., Chang, R.-H., Tang, W., Chang, M.-H., Wang, I.-H., et al. (2023) · Journal of Biomedical Science · doi:10.1186/s12929-023-00980-w · Cited by 4
“4c, arrow) with a diameter of 80–100 nm, the size of which was similar to the size of SARS-CoV-2 [25, 26].”
ResultDeng, M., Zhang, C., Yan, W., Chen, L., He, B., & Li, Y. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052850 · Cited by 4
“…inhibit its spread, replication, and proliferation, and to curb the continued spread of the epidemic world-wide, researchers have used sub-atomic resolution three-dimensional averaging (STA) and cryo-electron tomography (Cryo-ET) techniques to reveal the true molecular structure of SARS-CoV-2 [14].”
BackgroundRoy, R. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1292588 · Cited by 4
Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike
Oliveira, A. S. F., Kearns, F. L., Rosenfeld, M. A., Casalino, L., Tulli, L., Berger, I., Schaffitzel, C., Davidson, A. D., Amaro, R. E., & Mulholland, A. J. (2024) · eLife · doi:10.7554/elife.97313.3 · Cited by 7
Coronavirus disease 2019 vaccines: landscape of global studies and potential risks
Jiang, H.-D., Tao, Y., Jia, S., Li, J., & Zhu, F. (2021) · Chinese Medical Journal · doi:10.1097/cm9.0000000000001688 · Cited by 4
“Recent studies have shown that the heptad repeat 2 (HR2) in the S2 subunit may trigger a metastable state of the S protein and promote conformational changes, thereby achieving immune escape.([33]) Animal experiments have also confirmed that an HR2deficient SARS-CoV-2 S protein can induce higher neutralizing antibody…”
BackgroundIsoExplorer: an isosurface-driven framework for 3D shape analysis of biomedical volume data
Dai, H., Tao, Y., He, X., & Lin, H. B. (2021) · Journal of Visualization · doi:10.1007/s12650-021-00770-2 · Cited by 4
“…5159 H-CoV Spike (Park et al. 2019) 280 (cid:4) 280 (cid:4) 280 3149 PD-CoV Spike (Shang et al. 2018) 256 (cid:4) 256 (cid:4) 256 2868 SARS-CoV-2 (Yao et al. 2020) 512 (cid:4) 512 (cid:4) 512 3071 SARS-CoV-2 Spike up (Melero et al. 2020) 432 (cid:4) 432 (cid:4) 432 10 SARS-CoV-2 Spike down 1…”
BackgroundInfluentialNanomaterials and Biosensing Technology for the SARS-CoV-2 Detection
Yanyan, L. I., Peng, Y., Lin, C., Luo, X., Teng, Z., ZHANG, X., HUANG, Z., & Yang, Y. (2022) · Journal of Inorganic Materials · doi:10.15541/jim20220218 · Cited by 4
Mechanics of diffusion-mediated budding and implications for virus replication and infection
Bacca, M. (2022) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0525 · Cited by 4
“The input energy is extracted from Figure 3b, and the predictions are compared against the observed median virion sizes for SARS-CoV-1 & 2 [7-9], HIV-1 [10], Flu [11-12], and HCV (Hepatitis C) [13-14].”
BackgroundMethodInfluentialThe “LLQY” Motif on SARS-CoV-2 Spike Protein Affects S Incorporation into Virus Particles
Du, S., Xu, W., Wang, Y., Li, L., Hao, P., Tian, M., Wang, M., Li, T., Wu, S.-P., Liu, Q., et al. (2022) · Journal of Virology · doi:10.1128/jvi.01897-21 · Cited by 5
“domains with three flexible hinges in the S2 subunit (4, 20).”
BackgroundSelf-citationMan, J., Man, L., Zhou, C., Li, J., Liang, S., Zhang, S., & Li, J. (2022) · Biosensors · doi:10.3390/bios12050294 · Cited by 4
“To simulate the size of the COVID-19 virus [35], 100 nm sized fluorescent Nile Red nanoparticles were used to simulate the virus within the exhaled droplets since it was difficult to receive the required qualifications to perform virus-spread experiments.”
MethodMorphological Features and Divergence of SARS-CoV 2 and SARS-CoV Virus Using TEM ImagesPreprint
Taha, B. A., Mashhadany, Y. I. M. A., Al-Jubouri, Q., Zan, M. S. D., Luo, Y., Li, M., & Arsad, N. (2022) · Research Square · doi:10.21203/rs.3.rs-1336182/v1 · Cited by 4
Wang, D., Li, J., Wang, L., Cao, Y., Li, S., & Song, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.31.478415 · Cited by 4
“Thus, the RNP unit structure was obtained by aligning five N protein dimers into the density map (EMD-30429) (Fig.”
BackgroundMethodResultInfluentialSelf-citationAssembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acidPreprint
Zhao, H., Syed, A. M., Khalid, M. M., Nguyen, A., Ciling, A., Wu, D., Yau, W., Srinivasan, S., Esposito, D., Doudna, J. A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.22.568361 · Cited by 4
Hoffmann, T., Michel, J., Nitsche, A., Mache, C., Schulze, J., Wolff, T., & Laue, M. M. (2024) · Scientific Data · doi:10.1038/s41597-024-04182-3 · Cited by 4
Resurrection of the Helical Hairpin Hypothesis for Understanding Coronavirus Fusion
Lall, S., Vijayasarathy, M., Joshi, N. V., & Balaram, P. N. (2025) · The Journal of Membrane Biology · doi:10.1007/s00232-025-00350-7 · Cited by 3
“1A) (Ke et al. 2020; Turonova et al. 2020; Yao et al. 2020).”
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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