The DOI matches its Crossref record; 76 of the 82 references it cites were found in a registry or an index.
Molecular Architecture of the SARS-CoV-2 Virus
Open accessPublished version of a preprint
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952 · cited 1×
“PDB: 6XR8 was prepared in VMD (Humphrey et al., 1996) for the MDFF, which was performed in vacuum ll”
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,882 · cited 2×
“Fitting Atomic models (PDB accession code 6XR8, 6VYB, 6XRA) of the pre- and postfusion S were rigidly fitted to the corresponding densities using the Fit in Map tool (Pettersen et al., 2004).”
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., et al. (2020) · Nature · doi:10.1038/s41586-020-2012-7 · Cited by 21,969 · cited 3×
“The causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel b-coronavirus (Lu et al., 2020; Wu et al., 2020; Zhou et al., 2020).”
Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.052 · Cited by 20,286 · cited 2×
“The S protein binds to the cellular surface receptor angiotensin-converting enzyme 2 (ACE2) through the receptor binding domain (RBD), an essential step for membrane fusion (Hoffmann et al., 2020; Lan et al., 2020; Shang et al., 2020; Wang et al., 2020; Yan et al., 2020; Zhou et al., 2020).”
BackgroundSelf-citationScalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914 · cited 1×
“12 (Phillips et al., 2005) and the CHARMM36 force field (MacKerell et al.”
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,429 · cited 1×
“, 2005) and the CHARMM36 force field (MacKerell et al., 1998).”
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30251-8 · Cited by 11,907 · cited 2×
“The causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel b-coronavirus (Lu et al., 2020; Wu et al., 2020; Zhou et al., 2020).”
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688 · cited 2×
“The causative pathogen, SARS-CoV-2, is a novel β-coronavirus (Lu et al., 2020; Wu et al., 2020; Zhou et al., 2020).”
Self-citationCryo-EM structure of the 2019-nCoV spike in the prefusion conformation
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897 · cited 12×
“Several prefusion conformations have been resolved for the S protein, where the three RBDs display distinct orientations: up or down (Walls et al., 2020; Wrapp et al., 2020).”
BackgroundInfluentialStructure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586 · cited 12×
“Native Structures of S in the Prefusion Conformation The native structures of S in the ‘‘RBD down’’ and ‘‘one RBD up’’ conformations were similar to the rigidly fitted recombinant protein structures (PDB: 6XR8, 6VYB; Cai et al., 2020; Walls et al., 2020), except for the N terminus domain (NTD).”
Influential
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
Advances in COVID-19 mRNA vaccine development
Fang, E., Liu, X., Li, M., Zhang, Z., Song, L., Zhu, B., Wu, X., Liu, J., Zhao, D., & Li, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00950-y · Cited by 601
Self-citationCOVID-19: A Global Challenge with Old History, Epidemiology and Progress So Far
Khan, M., Adil, S. F., Alkhathlan, H. Z., Tahir, M. N., Saif, S., Khan, M., & Khan, S. T. (2020) · Molecules · doi:10.3390/molecules26010039 · Cited by 665
“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
Legrand, M. M., Bell, S., Forni, L. G., Joannidis, M., Koyner, J. L., Liu, K. D., & Cantaluppi, V. (2021) · Nature Reviews Nephrology · doi:10.1038/s41581-021-00452-0 · Cited by 527
Lu, S., Ye, Q., Singh, D., Cao, Y., Diedrich, J. K., Yates, J. R., Villa, E., Cleveland, D. W., & Corbett, K. D. (2021) · Nature Communications · doi:10.1038/s41467-020-20768-y · Cited by 464
Structural impact on SARS-CoV-2 spike protein by D614G substitution
Zhang, J., Cai, Y., Xiao, T., Lu, J., Peng, H., Sterling, S. M., Walsh, R. M., Rits‐Volloch, S., Zhu, H., Woosley, A. N., et al. (2021) · Science · doi:10.1126/science.abf2303 · Cited by 407
Self-citationCarlson, C. R., Asfaha, J. B., Ghent, C. M., Howard, C. J., Hartooni, N., Safari, M., Frankel, A. D., & Morgan, D. O. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.025 · Cited by 379
Isotropic reconstruction for electron tomography with deep learning
Liu, Y.-T., Zhang, H., Wang, H., Tao, C.-L., Bi, G., & Zhou, Z. H. (2022) · Nature Communications · doi:10.1038/s41467-022-33957-8 · Cited by 397
Zheng, S. Q., Wolff, G., Greenan, G. A., Chen, Z., Faas, F. G. A., Bárcena, M., Koster, A. J., Cheng, Y., & Agard, D. A. (2022) · Journal of Structural Biology X · doi:10.1016/j.yjsbx.2022.100068 · Cited by 330
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 301
“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 314
“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 292
Bagdonaite, I., Malaker, S. A., Polasky, D. A., Riley, N. M., Schjoldager, K. T.-B. G., Vakhrushev, S. Y., Halim, A., Aoki-Kinoshita, K. F., Nesvizhskii, A. I., Bertozzi, C. R., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00128-4 · Cited by 271
Structure of SARS-CoV-2 spike protein
Zhang, J., Xiao, T., Cai, Y., & Chen, B. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.08.010 · Cited by 261
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 222
“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 220
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 227
Liu, H., Wu, N. C., Yuan, M., Bangaru, S., Torres, J. L., Caniels, T. G., van Schooten, J., Zhu, X., Lee, C.-C. D., Brouwer, P. J. M., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.10.023 · Cited by 201
“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. S., Stone, H., Lu, M., Anand, S. P., Beaudoin-Bussières, G., Symmes, K., Benlarbi, M., Ding, S., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.08.015 · Cited by 212
“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 234
“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
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 226
SARS-CoV-2 biology and host interactions
Steiner, S., Kratzel, A., Barut, G. T., Lang, R. M., Moreira, É. A., Thomann, L., Kelly, J. N., & Thiel, V. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-023-01003-z · Cited by 235
“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 198
“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 204
Wang, R., Chen, J., Gao, K., Hozumi, Y., Yin, C., & Wei, G. (2021) · Communications Biology · doi:10.1038/s42003-021-01754-6 · Cited by 201
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 231
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 184
“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 193
Two-Component Spike Nanoparticle Vaccine Protects Macaques from SARS-CoV-2 Infection
Brouwer, P. J. M., Brinkkemper, M., Maisonnasse, P., Dereuddre‐Bosquet, N., Grobben, M., Claireaux, M. A. F., de Gast, M., Marlin, R., Chesnais, V., Diry, S., et al. (2020) · Cell · doi:10.1016/j.cell.2021.01.035 · Cited by 188
Self-citationThe humoral response and antibodies against SARS-CoV-2 infection
Qi, H., Liu, B., Wang, X., & Zhang, L. (2022) · Nature Immunology · doi:10.1038/s41590-022-01248-5 · Cited by 195
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 206
“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
Bernard, I., Limonta, D., Mahal, L. K., & Hobman, T. C. (2020) · Viruses · doi:10.3390/v13010029 · Cited by 187
Zhu, X. Q., Mannar, D., Srivastava, S. S., Berezuk, A., Demers, J., Saville, J. W., Leopold, K., Li, W., Dimitrov, D. S., Tuttle, K. S., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001237 · Cited by 183
Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress
Mendonça, L., Howe, A., Gilchrist, J. B., Sheng, Y., Sun, D., Knight, M. L., Zanetti-Domingues, L. C., Bateman, B. C., Krebs, A.-S., Chen, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-021-24887-y · Cited by 188
A multiscale coarse-grained model of the SARS-CoV-2 virion
Yu, A., Pak, A. J., He, P., Monje‐Galvan, V., Casalino, L., Gaieb, Z., Dommer, A. C., Amaro, R. E., & Voth, G. A. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.10.048 · Cited by 169
Zhang, Z., Pandey, R., Li, J., Gu, J., White, D., Stacey, H. D., Ang, J. C., Steinberg, C., Capretta, A. A., Filipe, C. D. M., et al. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202110819 · Cited by 167
Self-citationSARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA
Jack, A., Ferro, L. S., Trnka, M. J., Wehri, E., Nadgir, A., Nguyenla, X. H., Fox, D., Costa, K., Stanley, S. A., Schaletzky, J., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001425 · Cited by 161
Laue, M. M., Kauter, A., Hoffmann, T., Møller, L. F., Michel, J., & Nitsche, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-82852-7 · Cited by 164
Livanos, A. E., Jha, D., Cossarini, F., Gonzalez-Reiche, A. S., Tokuyama, M. A., Aydillo, T., Parigi, T. L., Ladinsky, M. S., Ramos, I., Dunleavy, K. A., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.02.056 · Cited by 163
Peng, R., Wu, L.-A., Wang, Q., Qi, J., & Gao, G. F. (2021) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2021.06.001 · Cited by 168
The structural basis of accelerated host cell entry by SARS‐CoV‐2†
Seyran, M., Takayama, K., Uversky, V. N., Lundstrom, K. H., Palù, G., Sherchan, S. P., Attrish, D., Rezaei, N., Aljabali, A. A. A., Ghosh, S., et al. (2020) · FEBS Journal · doi:10.1111/febs.15651 · Cited by 161
Saichi, M., Ladjemi, M. Z., Korniotis, S., Rousseau, C., Hamou, Z. A., Massenet-Regad, L., Amblard, E., Noël, F., Marie, Y., Bouteiller, D., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00681-2 · Cited by 159
Kamel, W., Noerenberg, M., Cerikan, B., Chen, H., Järvelin, A. I., Kammoun, M., Lee, Y. S., Ni, S., García-Moreno, M., Andrejeva, A., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.05.023 · Cited by 157
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 155
“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 222
“…(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
Graham, C., Seow, J., Huettner, I., Khan, H., Kouphou, N., Acors, S., Winstone, H., Pickering, S., Galão, R. P., Dupont, L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.023 · Cited by 155
“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
Self-citationFocosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 150
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 150
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 144
“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 141
“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 149
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
Li, W., Chen, Y., Prévost, J., Ullah, I., Lu, M., Gong, S. Y., Tauzin, A., Gasser, R., Vézina, D., Anand, S. P., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110210 · Cited by 128
“…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 129
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 130
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 132
“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 138
“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 124
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 121
“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 121
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 121
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 117
“(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
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 106
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 110
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 306
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
“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
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 93
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
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
“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
“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 104
“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 89
“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 91
“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 85
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 86
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 92
Inkjet Printing: A Viable Technology for Biosensor Fabrication
Hussain, A., Abbas, N., & Ali, A. (2022) · Chemosensors · doi:10.3390/chemosensors10030103 · Cited by 94
Wang, J., Chen, D., Huang, W., Yang, N., Yuan, Q., & Yang, Y. (2023) · Exploration · doi:10.1002/exp.20210027 · Cited by 88
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 92
“(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 93
“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 82
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 78
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
Wang, J., Shi, C., Xu, Q., & Yin, H. H. (2021) · Cell Discovery · doi:10.1038/s41421-020-00240-3 · Cited by 87
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
Self-citationCai, T., Yu, Z., Wang, Z., Chen, L., & Richard, S. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100821 · Cited by 83
“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 78
Ye, F., Zhao, J., Xu, P. H., Liu, X., Yu, J. Q., Shangguan, W., Liu, J., Luo, X., Li, C., Ying, T., et al. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202100543 · Cited by 80
Jamison, D. A., Narayanan, S. A., Trovão, N. S., Guarnieri, J. W., Topper, M. J., Moraes‐Vieira, P. M., Zaksas, V., Singh, K. K., Wurtele, E. S., & Beheshti, A. (2022) · European Journal of Human Genetics · doi:10.1038/s41431-022-01108-8 · Cited by 95
“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 81
“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 79
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
