Numbers of viral proteins: 20 E pentamers (100 proteins) and 1000 M dimers (2000 proteins)
CitationYinon M Bar-On, Avi Flamholz, Rob Phillips, Ron Milo. Science Forum: SARS-CoV-2 (COVID-19) by the numbers. eLife 2020;9:e57309 DOI: 10.7554/eLife.57309
There are around 30 S trimers shown in this model. This number is based both on Turonova et al. 2020 and on Ke et al. 2020
CitationKe, Z., Oton, J., Qu, K. et al. Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature 588, 498–502 (2020). https://doi.org/10.1038/s41586-020-2665-2
Each S trimer is able to bend in a flexible manner. This bending is based on cryo-ET images from Ke et al. 2020 and Turonova et al. 2020
CitationBeata Turoňová, Mateusz Sikora, Christoph Schürmann, Wim J. H. Hagen, Sonja Welsch, Florian E. C. Blanc, Sören von Bülow, Michael Gecht, Katrin Bagola, Cindy Hörner, Ger van Zandbergen, Jonathan Landry, Nayara Trevisan Doimo de Azevedo, Shyamal Mosalaganti, Andre Schwarz, Roberto Covino, Michael D. Mühlebach, Gerhard Hummer, Jacomine Krijnse Locker, and Martin Beck. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science. 2020 Oct 9; 370(6513): 203–208. PMCID: PMC7665311
The animation shows the S protein undergoing a 'breathing' motion where different subunits are in the 'up' state at different times. The relative length of time that the subunits should spend in the up state was uncertain.
CitationWrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260-1263. doi: 10.1126/science.abb2507. Epub 2020 Feb 19. PMID: 32075877; PMCID: PMC7164637.
Full-length N protein model was downloaded from Zhang lab repository and arranged in octamers as described in Chen et al 2007. N and C terminus were rotated and moved relative to one another in the animation to avoid steric clashes. This assumes a flexible attachment between N and C lobes.
CitationChun-Yuan Chen, Chung-ke Chang, Yi-Wei Chang, Shih-Che Sue, Hsin-I Bai, Lilianty Riang, Chwan-Deng Hsiao, and Tai-huang Huang. Structure of the SARS Coronavirus Nucleocapsid Protein RNA-binding Dimerization Domain Suggests a Mechanism for Helical Packaging of Viral RNA. J Mol Biol. 2007 May 11; 368(4): 1075–1086.
ACE2 is created using PDB 6M17 and animated as having a flexible 'neck' to allow for a tilted angle when binding to S protein. Both monomeric and dimeric ACE2 is shown in the animation.http://www.rcsb.org/structure/6m17
Furin model was created using PDB 1P8J (catalytic and protease domain), with a 42nm linker to a transmembrane domain addedhttps://www.rcsb.org/structure/1p8j
00:29-00:50
event
ACE2 on the cell membrane capture S proteins when they are in the "up" state. In the animation, an ACE dimer is shown binding to a S protein. Whether all three S proteins need to be bound for infection to occur is not clear. The number of Spikes that are engaged by ACE2 during an entry event is also uncertain.
00:45-00:50
event
S proteins are cleaved by TMPRSS2 at the S2' site. In the animation, cleavages are indicated by flashes of light. S protein undergoes cleavage by furin at the S1/S2 site prior to being transported to the cell surface.
CitationDorothea Bestle, Miriam Ruth Heindl, Hannah Limburg, Thuy Van Lam van, Oliver Pilgram, Hong Moulton, David A. Stein, Kornelia Hardes, Markus Eickmann, Olga Dolnik, Cornelius Rohde, Stephan Becker, Hans-Dieter Klenk, Wolfgang Garten, Torsten Steinmetzer, Eva Böttcher-Friebertshäuser. TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-CoV-2 in human airway epithelial cells and provide promising drug targets. BioRxiv. https://doi.org/10.1101/2020.04.15.042085
S proteins transition to the pre-hairpin intermediate, with fusion peptide embedded in the host cell membrane.
01:00-01:10
structure
S protein prefusion structure is from PDB 6VSB (residues 816-1273). S protein pre-hairpin intermediate model was created and provided by Jason McLellan. The animated transition is speculative.https://www.rcsb.org/structure/6VSB
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S proteins transition to the post-fusion state.
01:10-01:18
structure
S protein postfusion structure is PDB 6M3W with missing residues modeled in using the pre-hairpin intermediate structure as a guide. The animated transition is speculative.https://www.rcsb.org/structure/6m3w
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event
Membrane fusion between the host cell membrane and the viral membrane occurs, and the viral RNA is deposited into the cell.
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Comments
Janet Iwasa:0:00We welcome any and all comments, suggestions, thoughts, criticisms!
on Tue, 28 Jul 2020 21:15:18 GMT
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Janet Iwasa:0:00Twitter user @EpicBear asks "Curious, do you have any temporal information to go with this animation?"
on Tue, 23 Feb 2021 15:50:01 GMT
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Margaret Lee:0:00captions?I'm sorry if I missed this earlier, but are there closed captions available for this video? I'd love to show it to students, but we must have captions to do so. Thanks!
on Thu, 11 Mar 2021 06:00:45 GMT
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Patrick Kearns:0:00The number of spike trimers and envelope pentamers seems ~correct as per the citations but the number of membrane proteins shown too few. Quick look with imageJ suggests ~220 membrane dimers visible, so would be ~2x or 3x as many as per the Neumann et al citation (1100 dimers per virion).
Extra-virion portion of the membrane protein may be a T independent antigen (https://www.medrxiv.org/content/10.1101/2022.07.11.22277368v1), hence my interest in this. Thanks for the model, very nice project.
on Mon, 18 Jul 2022 14:47:29 GMT
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Janet Iwasa:0:04Twitter user Chris Voltaire @Voltairos suggests "One useful addition would be a reference to RBD, if possible shown as a different color area on the spike."
on Tue, 23 Feb 2021 15:51:29 GMT
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Jen Rogers:0:12testing
on Thu, 16 Dec 2021 20:38:13 GMT
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Matthew Akamatsu:0:22furinLocalizationGolgiThis animation is so wonderful! Can you note somewhere about Furin's usual location (in the Golgi)? Its differential localization compared to TMPRSS2 came up in our cell biology course. Eg https://www.proteinatlas.org/ENSG00000140564-FURIN/subcellular#human
on Thu, 26 Oct 2023 05:31:14 GMT
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Hubert J. G.:0:29It would be nice to have rough time estimates for the events. Just something like the order of magnituted of the events.
on Sun, 18 Apr 2021 11:33:07 GMT
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Michael Sheikh:0:33There are not supposed to be multiple ACE2 receptors binding with the spike protein. It is one ace to one spike protein. Additionally the Spike protein needs to be in the up or primed position.
on Tue, 10 Aug 2021 00:35:07 GMT
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Janet Iwasa:0:46Arnaud Martin asks "Does TMPRSS2 target the "furin cleavage sites"?"
on Wed, 17 Feb 2021 21:26:57 GMT
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Brian Cady:0:47TMPRSS2bromhexineambroxolcamostatCould a variant of this video show TMPRSS2 inhibitor activity (e.g. Bromhexine, Ambroxol, Camostat)?
on Sun, 01 Aug 2021 18:24:50 GMT
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Janet Iwasa:0:53Twitter user @DrSteph820 asks "The animation shows s1 being left on the surface of the infected cell. Is this accurate? I had the impression that s1 was endocytosed with the viral particle"
on Thu, 18 Feb 2021 15:33:40 GMT
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Prashant Bharadwaj:1:02seems like the spike proteins are unbound to anything on the cell surface at this stage. How does the virus not diffuse away at this stage? (or does it diffuse sometimes)
Is this very transient phase, after which the trimmed spike anchors the cell membrane within a short time?
on Thu, 18 Feb 2021 00:14:59 GMT
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Matthew Akamatsu:1:03ACE2EndocytosisMembrane fusionOne of my favorite articles on SARS-CoV-2 evolution is Meng 2022, which shows that the Omicron variant preferentially enters cells through clathrin-mediated endocytosis:
https://doi.org/10.1038/s41586-022-04474-x Would it be possible to indicate the branching between these two possible pathways? One could even make the argument that the predominant version of SARS-CoV-2 is now mostly entering cells through endocytosis; it would probably be fun and instructive to see the endocytosis of a SARS-CoV-2 virion to scale
on Thu, 26 Oct 2023 05:38:19 GMT
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Janet Iwasa:1:04Twitter user Michael Lachmann (@mikha_ehl) comments that a similar animation was shown by Twitter user @EricTopol about a recent science paper: https://twitter.com/EricTopol/status/1362080258841710595
on Tue, 23 Feb 2021 15:56:16 GMT
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Sarah Croskell:1:20The script and the visual are not timed together. I knew what I was looking at/for but I still needed to back up four times to see the details. It would make it easier to follow.