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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The S protein is considered the main antigen for vaccine design.
“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]
The trimeric S protein on the surface of SARS-CoV-2 plays a key role in mediating host cell invasion.
“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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BackgroundMethodA thermostable, closed SARS-CoV-2 spike protein trimer
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“, 2017) reports, the N_NTD and N_CTD possibly form a reverse L-shaped unit; the N_CTD dimer was suggested to be an assembly unit of the RNP (Chen et al., 2007).”
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Self-citationRey, F. A., & Lok, S. (2018) · Cell · doi:10.1016/j.cell.2018.02.054 · Cited by 232 · cited 2× · see citing works
“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× · see citing works
“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 194 · cited 1× · see citing works
“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 193 · cited 2× · see citing works
“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 148 · cited 1× · see citing works
“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× · see citing works
“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× · see citing works
“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 125 · see citing works
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× · see citing works
“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 109 · cited 2× · see citing works
“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× · see citing works
“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).”
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 · see citing works
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× · see citing works
“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).”
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 76 · see citing works
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× · see citing works
“, 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× · see citing works
“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× · see citing works
“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× · see citing works
“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 · see citing works
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Mechanisms of SARS-CoV-2 entry into cells
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COVID-19 and the human innate immune system
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“, 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., Wachsmuth-Melm, M., Neufeldt, C., Cerikan, B., Stanifer, M., Boulant, S., Bartenschlager, R., & Chlanda, P. (2020) · Nature Communications · doi:10.1038/s41467-020-19619-7 · Cited by 638 · see citing works
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
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Advances in COVID-19 mRNA vaccine development
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Self-citationCOVID-19: A Global Challenge with Old History, Epidemiology and Progress So Far
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“9 kilobases in length, which is packed in ~80-nm-diameter lumen and contains fourteen open reading frames [92,93].”
BackgroundPathophysiology of COVID-19-associated acute kidney injury
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Structural impact on SARS-CoV-2 spike protein by D614G substitution
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Isotropic reconstruction for electron tomography with deep learning
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Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study
Hastie, K. M., Li, H., Bedinger, D., Schendel, S. L., Dennison, S. M., Li, K., Rayaprolu, V., Yu, X., Mann, C. J., Zandonatti, M. A., et al. (2021) · Science · doi:10.1126/science.abh2315 · Cited by 299 · see citing works
“A recent cryo-electron tomography study showed native Spike trimers on the SARS-CoV-2 virion surface tilt at variable degrees relative to the viral envelope ( 22 ).”
BackgroundStructural biology of SARS-CoV-2: open the door for novel therapies
Yan, W., Zheng, Y., Zeng, X., He, B., & Cheng, W. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00884-5 · Cited by 293 · see citing works
“Besides, HR2 partly becomes ordered and packs against the groove of HR1 coiled-coil with the formation of sixhelix-bundle (6HB) structure, which contribute to the fusion of virus and cell membrane.(34,35)”
BackgroundThe total number and mass of SARS-CoV-2 virions
Sender, R., Bar‐On, Y. M., Gleizer, S., Bernshtein, B., Flamholz, A. I., Phillips, R., & Milo, R. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024815118 · Cited by 278 · see citing works
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Structure of SARS-CoV-2 spike protein
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Self-citationStructural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
Cai, Y., Zhang, J., Xiao, T., Lavine, C. L., Rawson, S., Peng, H., Zhu, H., Anand, K., Tong, P., Gautam, A. K., et al. (2021) · Science · doi:10.1126/science.abi9745 · Cited by 219 · see citing works
“Remarkable progress in structural biology of the S protein has been achieved rapidly since the early stage of the pandemic, advancing our knowledge on the SARS-CoV-2 entry process considerably (15-28).”
BackgroundSelf-citationSARS-COV-2 Variants: Differences and Potential of Immune Evasion
Hirabara, S. M., Serdan, T. D. A., Gorjão, R., Masi, L. N., Pithon‐Curi, T. C., Covas, D. T., Curi, R., & Durigon, E. L. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.781429 · Cited by 216 · see citing works
Cellular host factors for SARS-CoV-2 infection
Baggen, J., Vanstreels, E., Jansen, S., & Daelemans, D. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00958-0 · Cited by 209 · see citing works
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“A recent cryoelectron tomography (cryo-ET) analysis demonstrated that the average distance between prefusion S on the viral surface is around 150 Å (Yao et al., 2020), which is comparable with the distance between the tip of the two antibody fragments (Fabs) on an IgG (typically around 100–150 Å, although longer dista…”
Self-citationUllah, I., Prévost, J., Ladinsky, M., Stone, H., Lu, M.-L., Anand, S., Beaudoin-Bussières, G., Symmes, K., Benlarbi, M., Ding, S.-L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.08.015 · Cited by 152 · see citing works
“Presumptive SARS-CoV-2 virions were identified from tomographic reconstructions of tissue samples by observing structures resembling virions described in cryo-electron tomography studies of purified SARS-CoV-2 and of SARS-CoV-2 in infected cells (Ke et al., 2020; Klein et al., 2020; Turo nová et al., 2020; Yao et al.,…”
Self-citationWu, W., Cheng, Y., Zhou, H. W., Sun, C., & Zhang, S. (2023) · Virology Journal · doi:10.1186/s12985-023-01968-6 · Cited by 213 · see citing works
“SARS‐CoV‐2 SARS-CoV-2 is a pleomorphic particle with a diameter of approximately 60–100 nm [26, 27].”
BackgroundSelf-citationZamzami, M. A., Rabbani, G., Ahmad, A., Basalah, A. A., Alsabban, W. H., Ahn, S. N., & Choudhry, H. (2021) · Bioelectrochemistry · doi:10.1016/j.bioelechem.2021.107982 · Cited by 211 · see citing works
The glycosylation in SARS-CoV-2 and its receptor ACE2
Gong, Y., Qin, S., Dai, L., & Tian, Z. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00809-8 · Cited by 207 · see citing works
SARS-CoV-2 biology and host interactions
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“Interactions between the N protein and the cytoplasmic tail of the M protein then presumably drive incorporation into new virions at the ER-to-Golgi intermediate compartment (ERGIC) 94,95 (Fig.”
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles
Lu, M., Uchil, P. D., Li, W., Zheng, D., Terry, D. S., Gorman, J., Shi, W., Zhang, B., Zhou, T., Ding, S., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.001 · Cited by 194 · see citing works
“in line with previous EM investigations (Cai et al., 2020; Henderson et al., 2020; Hsieh et al., 2020; Ke et al., 2020; Lan et al., 2020; McCallum et al., 2020; Shang et al., 2020; Walls et al., 2020; Wang et al., 2020; Wrobel et al., 2020; Yao et al., 2020), the RBD-down state is the most populated.”
The architecture of the SARS-CoV-2 RNA genome inside virion
Cao, C., Cai, Z., Xiao, X., Rao, J. Y., Chen, J., Hu, N., Yang, M., Xing, X., Wang, Y., Li, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22785-x · Cited by 206 · see citing works
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Structure of SARS-CoV-2 membrane protein essential for virus assembly
Zhang, Z., Nomura, N., Muramoto, Y., Ekimoto, T., Uemura, T., Liu, K., Yui, M., Kono, N., Aoki, J., Ikeguchi, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32019-3 · Cited by 203 · see citing works
Self-citationRecognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies
Yuan, M., Liu, H., Wu, N. C., & Wilson, I. A. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.10.012 · Cited by 181 · see citing works
“The average distance between prefusion S trimer of SARS-CoV-2 is around 150 Å [57], which is similar to other coronaviruses [58] and comparable to the distance spanning the tip of two Fabs on an IgG [53].”
Self-citationAI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
Casalino, L., Dommer, A. C., Gaieb, Z., de Barros, E. P., Sztain, T., Ahn, S.-H., Trifan, A., Brace, A., Bogetti, A. T., Clyde, A., et al. (2021) · The International Journal of High Performance Computing Applications · doi:10.1177/10943420211006452 · Cited by 187 · see citing works
Two-Component Spike Nanoparticle Vaccine Protects Macaques from SARS-CoV-2 Infection
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Self-citationThe humoral response and antibodies against SARS-CoV-2 infection
Qi, H., Liu, B., Wang, X.-Q., & Zhang, L.-Q. (2022) · Nature Immunology · doi:10.1038/s41590-022-01248-5 · Cited by 169 · see citing works
SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights
Kadam, S. B., Sukhramani, G. S., Bishnoi, P., Pable, A. A., & Barvkar, V. T. (2021) · Journal of Basic Microbiology · doi:10.1002/jobm.202000537 · Cited by 193 · see citing works
“Recently cryo‐electron microscopy revealed the structure of S protein suggesting it can make hinge‐like movement resulting into transitions between “up” and “down” confirmations [44,46,47].”
BackgroundEndothelium Infection and Dysregulation by SARS-CoV-2: Evidence and Caveats in COVID-19
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Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress
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A multiscale coarse-grained model of the SARS-CoV-2 virion
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Self-citationSARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA
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The structural basis of accelerated host cell entry by SARS‐CoV‐2†
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Native-like SARS-CoV-2 Spike Glycoprotein Expressed by ChAdOx1 nCoV-19/AZD1222 Vaccine
Watanabe, Y., Mendonça, L., Allen, E. R., Howe, A., Lee, M., Allen, J. D., Chawla, H., Pulido, D., Donnellan, F. R., Davies, H. D., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00080 · Cited by 149 · see citing works
“A mixture of oligomannose/hybrid and complex-type sites were observed, with glycan sites such as N234, which are known to have stabilising effects on the RBD, preserving the predominantly oligomannose state reported in both recombinant proteins and viruses ( 5 , 27 , 35 ).”
Self-citationRespiratory aerosols and droplets in the transmission of infectious diseases
Pöhlker, M. L., Pöhlker, C., Krüger, O. O., Förster, J., Berkemeier, T., Elbert, W., Fröhlich‐Nowoisky, J., Pöschl, U., Bagheri, G., Bodenschatz, E., et al. (2023) · Reviews of Modern Physics · doi:10.1103/revmodphys.95.045001 · Cited by 206 · see citing works
“…(e.g., Fabian et al., 2011; Pitkaranta and Hayden, 1998), measles morbilliviruses (e.g., Liljeroos et al., 2011), SARS-CoV-2 (e.g., Ke et al., 2020; Yao et al., 2020; Zhu et al., 2020), influenza viruses (e.g., Enoki et al., 2012; Mosley and Wyckoff, 1946; Rossman and Lamb, 2011) and M.…”
BackgroundAn engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Chan, K. K., Tan, T. J. C., Narayanan, K. K., & Procko, E. (2021) · Science Advances · doi:10.1126/sciadv.abf1738 · Cited by 152 · see citing works
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“The S2 subunit, containing the fusion peptide, two heptad repeats (HR1 and HR2), the cytoplasmic tail and the transmembrane domain, is crucial for viral membrane fusion (Yao et al., 2020).”
Dugan, H. L., Stamper, C. T., Li, L., Changrob, S., Asby, N. W., Halfmann, P. J., Zheng, N.-Y., Huang, M., Shaw, D. G., Cobb, M. S., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.05.001 · Cited by 134 · see citing works
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Antibody-mediated neutralization of SARS-CoV-2
Gruell, H., Vanshylla, K., Weber, T., Barnes, C. O., Kreer, C., & Klein, F. (2022) · Immunity · doi:10.1016/j.immuni.2022.05.005 · Cited by 145 · see citing works
Tunneling nanotubes provide a route for SARS-CoV-2 spreading
Pepe, A., Pietropaoli, S., Vos, M. R. J., Spaeth, G. B., & Zurzolo, C. (2022) · Science Advances · doi:10.1126/sciadv.abo0171 · Cited by 138 · see citing works
“6, D to F and J to L, and movies S1 and S2) in accordance with recent cryo-EM data for the virus isolated from infected cells ( 55 – 57 ) and in situ cryo-ET of cryo-focused ion beam (cryo-FIB) in milled infected cells ( 45 ).”
Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins
Zhang, Y., Zhao, W., Mao, Y., Chen, Y., Wang, S., Zhong, Y., Su, T., Gong, M., Du, D., Lu, X., et al. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra120.002295 · Cited by 139 · see citing works
“Almost all 22 glycosites were modified with the complex-type N-glycans, which is highly consistent with the findings in our study (36).”
Self-citationInteractions between SARS-CoV-2 N-Protein and α-Synuclein Accelerate Amyloid Formation
Semerdzhiev, S. A., Fakhree, M. A. A., Segers‐Nolten, I. M. J., Blum, C., & Claessens, M. M. A. E. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.1c00666 · Cited by 143 · see citing works
Castaño, N., Cordts, S. C., Jalil, M. K., Zhang, K. S., Koppaka, S., Bick, A., Paul, R., & Tang, S. K. Y. (2021) · ACS Omega · doi:10.1021/acsomega.0c06335 · Cited by 148 · see citing works
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“…cryo electron microscopy (SP cryoEM) of a soluble trimer comprising most of the ec-todomain (Walls et al., 2020; Wrapp et al., 2020), as well as by cryo-electron tomography (cryoET) and SP cryoEM of native virus particles (Ke et al., 2020; Turo (cid:2) nova´ et al., 2020; Yao et al., 2020).”
Self-citationS-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Mesquita, F. S., Abrami, L., Sergeeva, O. A., Turelli, P., Qing, E., Kunz, B., Raclot, C., Montoya, J. P., Abriata, L. A., Gallagher, T., et al. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.09.016 · Cited by 126 · see citing works
Li, J., Zhang, Z., Gu, J., Stacey, H. D., Ang, J. C., Capretta, A. A., Filipe, C. D. M., Mossman, K. L., Balion, C. M., Salena, B. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab574 · Cited by 129 · see citing works
Self-citationCharacterization of the SARS‐CoV ‐2 E Protein: Sequence, Structure, Viroporin, and Inhibitors
Cao, Y., Yang, R., Lee, I., Zhang, W., Sun, J., Wang, W., & Meng, X. (2021) · Protein Science · doi:10.1002/pro.4075 · Cited by 126 · see citing works
“Viral structural proteins, including the S, E, M, and N proteins, are embedded in viral lipids.(16,17) The S protein has an immune recognition site and binds to the surface receptor during the process of entering the host cell; it is the most important protein for viral entry into cells.”
Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19
Wu, C., Yin, W., Jiang, Y., & Xu, H. E. (2022) · Acta Pharmacologica Sinica · doi:10.1038/s41401-021-00851-w · Cited by 127 · see citing works
“As described in the cryo-ET virion structure, the RNP is close to the inner membrane of the virus capsule, indicating that it is feasible to interact with membrane proteins like M and E proteins in terms of space proximity [119].”
BackgroundMethodInfluentialStructural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants
Mittal, A., Khattri, A., & Verma, V. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010260 · Cited by 121 · see citing works
Hunt, A. C., Case, J. B., Park, Y., Cao, L., Wu, K., Walls, A. C., Liu, Z., Bowen, J. E., Yeh, A. H.-W., Saini, S., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abn1252 · Cited by 116 · see citing works
“We next determined how the designed multivalent proteins engage multiple RBDs on a single S trimer; multivalent engagement on a virion typically requires binding of a single S trimer due to the relatively sparse S distribution ( 47 – 49 ).”
BackgroundThe role of cell surface sialic acids for SARS-CoV-2 infection
Sun, X. (2021) · Glycobiology · doi:10.1093/glycob/cwab032 · Cited by 120 · see citing works
He, L., Lin, X., Wang, Y., Abraham, C., Sou, C., Ngo, T., Zhang, Y., Wilson, I. A., & Zhu, J. (2021) · Science Advances · doi:10.1126/sciadv.abf1591 · Cited by 117 · see citing works
Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane
Shi, W. K., Cai, Y., Zhu, H., Peng, H., Voyer, J. E., Rits‐Volloch, S., Cao, H., Mayer, M. L., Song, K., Xu, C., et al. (2023) · Nature · doi:10.1038/s41586-023-06273-4 · Cited by 114 · see citing works
“(20, 21), as well as those of the S proteins present on chemically inactivated SARS-CoV-2 virions (22-25), were subsequently determined, revealing additional structural details.”
BackgroundSelf-citationHan, C., Li, W., Li, Q., Xing, W., Luo, H., Ji, H., Fang, X., Luo, Z., & Zhang, L. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113922 · Cited by 111 · see citing works
COVID-19 and the Vasculature: Current Aspects and Long-Term Consequences
Martínez-Salazar, B., Holwerda, M., Stüdle, C., Piragyte, I., Mercader, N., Engelhardt, B., Rieben, R., & Döring, Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.824851 · Cited by 102 · see citing works
Low-Cost Biosensor Technologies for Rapid Detection of COVID-19 and Future Pandemics
de Araujo, W. R., Lukas, H., Torres, M. D. T., Gao, W. F., & de la Fuente‐Núñez, C. (2024) · ACS Nano · doi:10.1021/acsnano.3c01629 · Cited by 102 · see citing works
Automated detection and forecasting of COVID-19 using deep learning techniques: A review
Shoeibi, A., Khodatars, M., Jafari, M., Ghassemi, N., Sadeghi, D., Moridian, P., Khadem, A. A., Alizadehsani, R., Hussain, S., Zare, A., et al. (2024) · Neurocomputing · doi:10.1016/j.neucom.2024.127317 · Cited by 297 · see citing works
An overview on nanoparticle-based strategies to fight viral infections with a focus on COVID-19
Yasamineh, S., Kalajahi, H. G., Yasamineh, P., Yazdani, Y., Gholizadeh, O., Tabatabaie, R., Afkhami, H., Davodabadi, F., farkhad, A. K., Pahlevan, D., et al. (2022) · Journal of Nanobiotechnology · doi:10.1186/s12951-022-01625-0 · Cited by 102 · see citing works
“including shedding its S1 subunit and incorporating the fusion peptide (FP) in the host cell membrane [29].”
BackgroundO-glycosylation pattern of the SARS-CoV-2 spike protein reveals an “O-Follow-N” rule
Tian, W., Li, D., Zhang, N., Bai, G., Yuan, K., Xiao, H., Gao, F., Yang, C., Wong, C. C. L., & Gao, G. F. (2021) · Cell Research · doi:10.1038/s41422-021-00545-2 · Cited by 98 · see citing works
The SARS-CoV-2 spike protein: balancing stability and infectivity
Berger, I., & Schaffitzel, C. (2020) · Cell Research · doi:10.1038/s41422-020-00430-4 · Cited by 96 · see citing works
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins
Tugaeva, K. V., Hawkins, D. E. D. P., Smith, J. L. R., Bayfield, O. W., Ker, D.-S., Sysoev, A. A., Klychnikov, O. I., Antson, A. A., & Sluchanko, N. N. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166875 · Cited by 95 · see citing works
SARS-CoV-2 Envelope (E) protein interacts with PDZ-domain-2 of host tight junction protein ZO1
Shepley‐McTaggart, A., Sagum, C. A., Oliva, I. B., Rybakovsky, E., DiGuilio, K., Liang, J., Bedford, M. T., Cassel, J. A., Sudol, M., Mullin, J. M., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251955 · Cited by 90 · see citing works
“The Spike (S), Membrane (M), Nucleocapsid (N), and Envelope (E) proteins are the four virion structural proteins that are encoded within the 3 end of the viral RNA genome [2, 3, 5, 15, 16].”
BackgroundBessa, L. M., Guseva, S., Camacho‐Zarco, A. R., Salvi, N., Maurin, D., Mariño, L., Botova, M., Malki, A., Nanao, M., Jensen, M. R., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm4034 · Cited by 94 · see citing works
“Electron tomography identified numerous N-RNA complexes within SARS-CoV-2 virions, apparently associated with different segments of the 35-kb genomes (19, 20).”
BackgroundSARS-CoV-2 and the Host Cell: A Tale of Interactions
Pizzato, M., Baraldi, C., Sopetto, G. B., Finozzi, D., Gentile, C., Gentile, M. D., Marconi, R., Paladino, D., Raoss, A., Riedmiller, I., et al. (2022) · Frontiers in Virology · doi:10.3389/fviro.2021.815388 · Cited by 94 · see citing works
“The evidence that some individual vRNPs are oriented on the viral envelope in an “eggs-in-a-nest” shaped assembly supports the role of specific M-N interactions driving packaging of new virions (237).”
BackgroundRoden, C., Dai, Y., Giannetti, C. A., Seim, I., Lee, M., Sealfon, R. S. G., McLaughlin, G. A., Boerneke, M. A., Iserman, C., Wey, S. A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac596 · Cited by 94 · see citing works
“Based on high-resolution cryo-EM tomography, the genome of SARS CoV-2 is arranged inside virions in a socalled ‘birds-nest’ arrangement with ‘eggs’ made of RNP complexes that are ∼14–20 nm (65,66).”
BackgroundMethodPhase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions
Cascarina, S. M., & Ross, E. D. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101677 · Cited by 88 · see citing works
“Locally ordered RNPs may be further organized into more complex arrangements via clustering of RNPs in particular stoichiometries and geometries (3, 4), although other evidence and prior models of the SARS-CoV N protein suggest a more linear, helical RNP arrangement (2, 5, 6).”
Saville, J. W., Mannar, D., Zhu, X. Q., Srivastava, S. S., Berezuk, A., Demers, J., Zhou, S., Tuttle, K. S., Sekirov, I., Kim, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28324-6 · Cited by 93 · see citing works
Harbison, A. M., Fogarty, C. A., Phung, T. K., Satheesan, A., Schulz, B. L., & Fadda, E. (2021) · Chemical Science · doi:10.1039/d1sc04832e · Cited by 87 · see citing works
A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors
Oliveira, A. S. F., Ibarra, A. Á., Bermúdez, I., Casalino, L., Gaieb, Z., Shoemark, D. K., Gallagher, T. C., Sessions, R. B., Amaro, R. E., & Mulholland, A. J. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.01.037 · Cited by 88 · see citing works
Inkjet Printing: A Viable Technology for Biosensor Fabrication
Hussain, A., Abbas, N., & Ali, A. (2022) · Chemosensors · doi:10.3390/chemosensors10030103 · Cited by 91 · see citing works
Wang, J., Chen, D., Huang, W., Yang, N., Yuan, Q., & Yang, Y. (2023) · Exploration · doi:10.1002/exp.20210027 · Cited by 88 · see citing works
A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions
Liu, Y., Zhang, X., Liu, J., Xia, H., Zou, J., Muruato, A. E., Periasamy, S., Kurhade, C., Plante, J. A., Bopp, N. E., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31930-z · Cited by 87 · see citing works
“(2)Generate reporter viruseswith accessory ORF deletions.”
A structural view of the SARS-CoV-2 virus and its assembly
Hardenbrook, N. J., & Zhang, P. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.11.011 · Cited by 85 · see citing works
“Because of the limited resolution, it remains unclear how the individual N proteins and RNA are organized within the vRNP [24 ,72].”
Extracellular Vimentin as a Target Against SARS‐CoV‐2 Host Cell Invasion
Suprewicz, Ł., Swoger, M., Gupta, S., Piktel, E., Byfield, F. J., Iwamoto, D. V., Germann, D., Reszeć, J., Marcińczyk, N., Carroll, R. J., et al. (2021) · Small · doi:10.1002/smll.202105640 · Cited by 80 · see citing works
Yang, Z., Han, Y., Ding, S., Shi, W., Zhou, T., Finzi, A., Kwong, P. D., Mothes, W., & Lu, M. (2022) · mBio · doi:10.1128/mbio.03227-21 · Cited by 77 · see citing works
Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China
Yang, L., & Wang, Z. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115503 · Cited by 85 · see citing works
Wang, J., Shi, C., Xu, Q., & Yin, H. H. (2021) · Cell Discovery · doi:10.1038/s41421-020-00240-3 · Cited by 84 · see citing works
Wu, Y., Huang, X., Yuan, L., Wang, S., Zhang, Y., Xiong, H., Chen, R., Ma, J., Qi, R., Nie, M., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abg1143 · Cited by 82 · see citing works
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“The primary role of betacoronavirus N protein is the packaging of the viral genome into helical ribonucleoprotein complexes (6).”
Choi, Y. K., Cao, Y., Frank, M., Woo, H., Park, S., Yeom, M. S., Croll, T. I., Seok, C., & Im, W. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01144 · Cited by 77 · see citing works
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“Coronaviruses are named as such because the S proteins resemble a halo or corona on scanning electron microscope imagery [3].”
BackgroundTopography, Spike Dynamics, and Nanomechanics of Individual Native SARS-CoV-2 Virions
Kiss, B., Kis, Z., Pályi, B., & Kellermayer, M. (2021) · Nano Letters · doi:10.1021/acs.nanolett.0c04465 · Cited by 80 · see citing works
“The flexural disorder observed here supports the interpretation of cryo-electron microscopic data (Ke et al., 2020; Turonova et al., 2020; Yao et al., 2020), revealing a high degree of spike flexibility.”
BackgroundResultInfluentialZhang, X., Liu, Y., Liu, J., Bailey, A. L., Plante, K. S., Plante, J. A., Zou, J., Xia, H., Bopp, N. E., Aguilar, P. V., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.044 · Cited by 80 · see citing works
Assessing Antigen Structural Integrity through Glycosylation Analysis of the SARS-CoV-2 Viral Spike
Brun, J., Vasiljević, S., Gangadharan, B., Hensen, M., Chandran, A. V., Hill, M. L., Kiappes, J. L., Dwek, R. A., Alonzi, D. S., Struwe, W. B., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00058 · Cited by 89 · see citing works
“25 − 28 However, we identi fi ed O-glycosylation at T678 on S1 virus , which was absent on S recombinant ‑ trimer .”
- 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
- Physical Sciences › Materials Science › Materials Chemistry › 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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