A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predo...

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Veröffentlicht in:	Cell reports (Cambridge) Jg. 40; H. 8; S. 111276
Hauptverfasser:	Seow, Jeffrey, Khan, Hataf, Rosa, Annachiara, Calvaresi, Valeria, Graham, Carl, Pickering, Suzanne, Pye, Valerie E., Cronin, Nora B., Huettner, Isabella, Malim, Michael H., Politis, Argyris, Cherepanov, Peter, Doores, Katie J.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States Elsevier Inc 23.08.2022 The Author(s)
Schlagworte:	Antibodies, Neutralizing Antibodies, Viral antibody COVID-19 Cryoelectron Microscopy cryogenic electron microscopy Epitopes Humans hydrogen-deuterium exchange Neutralization Tests neutralizing epitope omicron SARS-CoV-2 Spike Glycoprotein, Coronavirus spike subdomain 1 Syndactyly Vaccination hydrogen-deuterium exchange CP: Immunology SARS-CoV-2 spike subdomain 1 antibody omicron CP: Microbiology neutralizing epitope cryogenic electron microscopy
ISSN:	2211-1247, 2211-1247
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Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. [Display omitted] •A neutralizing epitope on spike subdomain 1 (SD1) is identified•The SD1 epitope is conserved between current SARS-CoV-2 variants and SARS-CoV•SD1 antibodies arise from infection and vaccination•Cryo-EM reveals the SD1 epitope is occluded on many SARS-CoV-2 spike structures Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike.
AbstractList	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. [Display omitted] •A neutralizing epitope on spike subdomain 1 (SD1) is identified•The SD1 epitope is conserved between current SARS-CoV-2 variants and SARS-CoV•SD1 antibodies arise from infection and vaccination•Cryo-EM reveals the SD1 epitope is occluded on many SARS-CoV-2 spike structures Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike.
ArticleNumber	111276
Author	Cherepanov, Peter Calvaresi, Valeria Graham, Carl Seow, Jeffrey Cronin, Nora B. Rosa, Annachiara Pye, Valerie E. Khan, Hataf Pickering, Suzanne Malim, Michael H. Politis, Argyris Huettner, Isabella Doores, Katie J.
Author_xml	– sequence: 1 givenname: Jeffrey surname: Seow fullname: Seow, Jeffrey organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 2 givenname: Hataf surname: Khan fullname: Khan, Hataf organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 3 givenname: Annachiara surname: Rosa fullname: Rosa, Annachiara organization: Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK – sequence: 4 givenname: Valeria surname: Calvaresi fullname: Calvaresi, Valeria organization: Department of Chemistry, King’s College London, London, UK – sequence: 5 givenname: Carl surname: Graham fullname: Graham, Carl organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 6 givenname: Suzanne surname: Pickering fullname: Pickering, Suzanne organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 7 givenname: Valerie E. surname: Pye fullname: Pye, Valerie E. organization: Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK – sequence: 8 givenname: Nora B. surname: Cronin fullname: Cronin, Nora B. organization: LonCEM Facility, The Francis Crick Institute, London, UK – sequence: 9 givenname: Isabella surname: Huettner fullname: Huettner, Isabella organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 10 givenname: Michael H. surname: Malim fullname: Malim, Michael H. organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK – sequence: 11 givenname: Argyris surname: Politis fullname: Politis, Argyris email: argyris.politis@kcl.ac.uk organization: Department of Chemistry, King’s College London, London, UK – sequence: 12 givenname: Peter surname: Cherepanov fullname: Cherepanov, Peter email: peter.cherepanov@crick.ac.uk organization: Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK – sequence: 13 givenname: Katie J. orcidid: 0000-0002-5507-1725 surname: Doores fullname: Doores, Katie J. email: katie.doores@kcl.ac.uk organization: Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
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Cites_doi	10.2807/1560-7917.ES.2020.25.42.2000685 10.1126/science.abb2507 10.1016/j.mex.2015.09.003 10.1016/j.bbapap.2011.12.007 10.1128/JVI.79.3.1635-1644.2005 10.1038/s41592-019-0459-y 10.1038/s42003-021-02399-1 10.1016/j.bbrc.2020.10.012 10.1128/JVI.02422-20 10.1038/s41591-020-1054-6 10.1038/nmeth.4169 10.1107/S2059798318006551 10.1016/j.chom.2021.02.003 10.1073/pnas.2022586118 10.1126/sciadv.abg7607 10.1371/journal.ppat.1008817 10.1038/s41586-020-2798-3 10.1093/bioinformatics/btaa677 10.1126/science.abf2303 10.1016/j.chom.2021.03.005 10.1128/JVI.00552-10 10.1111/joim.13372 10.1016/j.cell.2021.07.027 10.1038/s41577-020-0311-8 10.1107/S205225251801463X 10.1128/mbio.03798-21 10.1038/s41467-020-19231-9 10.1038/s41594-020-0468-7 10.1016/j.jmb.2003.07.013 10.1126/science.abc5902 10.1038/s41467-021-25480-z 10.1126/science.abc7520 10.1016/j.celrep.2022.110757 10.1038/nmeth.2115 10.1002/jcc.20084 10.1038/s41586-020-2852-1 10.1038/s41564-020-00813-8 10.1038/s41592-020-0914-9 10.1038/nmeth.4347 10.1107/S2059798319016577 10.1038/nmeth.4193 10.1038/s41401-020-0485-4 10.1038/s41586-020-2456-9 10.1002/pro.3330 10.3390/v13040628 10.1074/jbc.RA118.004343 10.1107/S2052252519007619 10.1007/s13361-013-0669-y 10.1002/rcm.4814 10.1016/j.immuni.2021.03.023 10.1107/S0907444906029799 10.1016/j.cell.2021.03.028 10.1038/s41586-020-2772-0 10.1016/j.jsb.2015.11.003 10.1038/s41586-020-2180-5 10.1016/j.it.2020.09.004 10.1107/S0907444904019158 10.1016/S1470-2045(21)00213-8 10.1016/j.tibs.2020.05.005 10.1038/nbt0997-871 10.1016/j.cell.2020.09.037 10.1016/j.celrep.2022.110348 10.1038/s41577-021-00542-x 10.1371/journal.pmed.0030237 10.1126/science.abi6226
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Keywords	hydrogen-deuterium exchange CP: Immunology SARS-CoV-2 spike subdomain 1 antibody omicron CP: Microbiology neutralizing epitope cryogenic electron microscopy
Language	English
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Faculty of Medicine, Wolfson Education Center, Hammersmith Campus, Imperial College London, Du Cane Road, London W12 0NN, UK These authors contributed equally Lead contact
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References	Ramaraj, Angel, Dratz, Jesaitis, Mumey (bib39) 2012; 1824 Huo, Mikolajek, Le Bas, Clark, Sharma, Kipar, Dormon, Norman, Weckener, Clare (bib23) 2021; 12 Pettersen, Goddard, Huang, Couch, Greenblatt, Meng, Ferrin (bib35) 2004; 25 Scheres (bib46) 2020; 76 Castro Dopico, Ols, Loré, Karlsson Hedestam (bib8) 2022; 291 Engen, Komives (bib15) 2020; 45 Zhang (bib63) 2016; 193 Rosenthal, Henderson (bib43) 2003; 333 Robbiani, Gaebler, Muecksch, Lorenzi, Wang, Cho, Agudelo, Barnes, Gazumyan, Finkin (bib40) 2020; 584 Tan, Baldwin, Davis, Williamson, Potter, Carragher, Lyumkis (bib49) 2017; 14 Gobeil, Janowska, McDowell, Mansouri, Parks, Stalls, Kopp, Manne, Li, Wiehe (bib17) 2021; 373 Seow, Graham, Hallett, Lechmere, Maguire, Huettner, Cox, Khan, Pickering, Roberts (bib47) 2022; 39 Zhang, Cai, Xiao, Lu, Peng, Sterling, Walsh, Rits-Volloch, Zhu, Woosley (bib62) 2021; 372 Barnes, Jette, Abernathy, Dam, Esswein, Gristick, Malyutin, Sharaf, Huey-Tubman, Lee (bib3) 2020; 588 Hurlburt, Seydoux, Wan, Edara, Stuart, Feng, Suthar, McGuire, Stamatatos, Pancera (bib24) 2020; 11 Huang, Yang, Xu, Xu, Liu (bib22) 2020; 41 van den Brink, Ter Meulen, Cox, Jongeneelen, Thijsse, Throsby, Marissen, Rood, Bakker, Gelderblom (bib56) 2005; 79 Gavor, Choong, Er, Sivaraman, Sivaraman (bib16) 2020; 41 Terwilliger, Ludtke, Read, Adams, Afonine (bib54) 2020; 17 Seow, Graham, Merrick, Acors, Pickering, Steel, Hemmings, O'Byrne, Kouphou, Galao (bib48) 2020; 5 Goswami, Devarakonda, Chalmers, Pascal, Spiegelman, Griffin (bib18) 2013; 24 Punjani, Rubinstein, Fleet, Brubaker (bib38) 2017; 14 Taylor, Adams, Hufford, de la Torre, Winthrop, Gottlieb (bib52) 2021; 21 Graham, Seow, Huettner, Khan, Kouphou, Acors, Winstone, Pickering, Galao, Dupont (bib19) 2021; 54 Cerutti, Guo, Zhou, Gorman, Lee, Rapp, Reddem, Yu, Bahna, Bimela (bib9) 2021; 29 Williams, Headd, Moriarty, Prisant, Videau, Deis, Verma, Keedy, Hintze, Chen (bib57) 2018; 27 Coales, E, Lee, Ma, Morrow, Hamuro (bib10) 2010; 24 Benton, Wrobel, Roustan, Borg, Xu, Martin, Rosenthal, Skehel, Gamblin (bib4) 2021; 118 Piccoli, Park, Tortorici, Czudnochowski, Walls, Beltramello, Silacci-Fregni, Pinto, Rosen, Bowen (bib36) 2020; 183 Afonine, Poon, Read, Sobolev, Terwilliger, Urzhumtsev, Adams (bib1) 2018; 74 Tanaka, Olson, Barnes, Higashide, Gonzalez, Taft, Richardson, Martin-Fernandez, Bogunovic, Gnanapragasam (bib50) 2022; 38 McCallum, Marco, Lempp, Tortorici, Pinto, Walls, Beltramello, Chen, Liu, Zatta (bib32) 2021 Hurt, Wheatley (bib25) 2021; 13 Sanchez-Garcia, Gomez-Blanco, Cuervo, Carazo, Sorzano, Vargas (bib44) 2021; 4 Brouwer, Caniels, van der Straten, Snitselaar, Aldon, Bangaru, Torres, Okba, Claireaux, Kerster (bib6) 2020; 369 Lechmere, Snell, Graham, Seow, Shalim, Charalampous, Alcolea-Medina, Batra, Nebbia, Edgeworth (bib30) 2022; 13 Zufferey, Nagy, Mandel, Naldini, Trono (bib66) 1997; 15 Rogers, Zhao, Huang, Beutler, Burns, He, Limbo, Smith, Song, Woehl (bib41) 2020; 369 Winstone, Lista, Reid, Bouton, Pickering, Galao, Kerridge, Doores, Swanson, Neil (bib58) 2021; 95 ter Meulen, van den Brink, Poon, Marissen, Leung, Cox, Cheung, Bakker, Bogaards, van Deventer (bib53) 2006; 3 Masson, Burke, Ahn, Anand, Borchers, Brier, Bou-Assaf, Engen, Englander, Faber (bib31) 2019; 16 Benton, Wrobel, Xu, Roustan, Martin, Rosenthal, Skehel, Gamblin (bib5) 2020; 588 Corti, Purcell, Snell, Veesler (bib11) 2021; 184 Kidmose, Juhl, Nissen, Boesen, Karlsen, Pedersen (bib26) 2019; 6 Thompson, Grayson, Paton, Bolton, Lourenço, Penman, Lee, Odon, Mongkolsapaya, Chinnakannan (bib55) 2020; 25 Zheng, Palovcak, Armache, Verba, Cheng, Agard (bib64) 2017; 14 Dixon (bib12) 2014 Grehan, Ferrara, Temperton (bib21) 2015; 2 Greaney, Loes, Crawford, Starr, Malone, Chu, Bloom (bib20) 2021; 29 Krammer (bib27) 2020; 586 Monin, Laing, Muñoz-Ruiz, McKenzie, Del Molino Del Barrio, Alaguthurai, Domingo-Vila, Hayday, Graham, Seow (bib34) 2021; 22 Lan, Ge, Yu, Shan, Zhou, Fan, Zhang, Shi, Wang, Zhang, Wang (bib28) 2020; 581 Wrobel, Benton, Xu, Roustan, Martin, Rosenthal, Skehel, Gamblin (bib60) 2020; 27 Tay, Poh, Rénia, MacAry, Ng (bib51) 2020; 20 Yuan, Liu, Wu, Wilson (bib61) 2021; 538 Emsley, Cowtan (bib14) 2004; 60 Min, Weiszmann, Johnstone, Wang, Yu, Romanow, Thibault, Li, Wang (bib33) 2018; 293 Carter, Fish, Jennings, Doores, Wellman, Seow, Acors, Graham, Timms, Kenny (bib7) 2020; 26 Lau, Claesen, Hansen, Politis (bib29) 2021; 37 Rosa, Pye, Graham, Muir, Seow, Ng, Cook, Rees-Spear, Parker, Dos Santos (bib42) 2021; 7 Pickering, Betancor, Galão, Merrick, Signell, Wilson, Kia Ik, Seow, Graham, Acors (bib37) 2020; 16 Wrapp, Wang, Corbett, Goldsmith, Hsieh, Abiona, Graham, McLellan (bib59) 2020; 367 Scheres, Chen (bib45) 2012; 9 Aricescu, Lu, Jones (bib2) 2006; 62 Doores, Burton (bib13) 2010; 84 Zivanov, Nakane, Scheres (bib65) 2019; 6 Robbiani (10.1016/j.celrep.2022.111276_bib40) 2020; 584 Pickering (10.1016/j.celrep.2022.111276_bib37) 2020; 16 Williams (10.1016/j.celrep.2022.111276_bib57) 2018; 27 Min (10.1016/j.celrep.2022.111276_bib33) 2018; 293 Gavor (10.1016/j.celrep.2022.111276_bib16) 2020; 41 Tan (10.1016/j.celrep.2022.111276_bib49) 2017; 14 Tanaka (10.1016/j.celrep.2022.111276_bib50) 2022; 38 Goswami (10.1016/j.celrep.2022.111276_bib18) 2013; 24 Piccoli (10.1016/j.celrep.2022.111276_bib36) 2020; 183 van den Brink (10.1016/j.celrep.2022.111276_bib56) 2005; 79 Zhang (10.1016/j.celrep.2022.111276_bib63) 2016; 193 Coales (10.1016/j.celrep.2022.111276_bib10) 2010; 24 Corti (10.1016/j.celrep.2022.111276_bib11) 2021; 184 Thompson (10.1016/j.celrep.2022.111276_bib55) 2020; 25 Lechmere (10.1016/j.celrep.2022.111276_bib30) 2022; 13 McCallum (10.1016/j.celrep.2022.111276_bib32) 2021 Zivanov (10.1016/j.celrep.2022.111276_bib65) 2019; 6 Yuan (10.1016/j.celrep.2022.111276_bib61) 2021; 538 Ramaraj (10.1016/j.celrep.2022.111276_bib39) 2012; 1824 Pettersen (10.1016/j.celrep.2022.111276_bib35) 2004; 25 Taylor (10.1016/j.celrep.2022.111276_bib52) 2021; 21 Huang (10.1016/j.celrep.2022.111276_bib22) 2020; 41 Gobeil (10.1016/j.celrep.2022.111276_bib17) 2021; 373 Rosa (10.1016/j.celrep.2022.111276_bib42) 2021; 7 Masson (10.1016/j.celrep.2022.111276_bib31) 2019; 16 Scheres (10.1016/j.celrep.2022.111276_bib46) 2020; 76 Carter (10.1016/j.celrep.2022.111276_bib7) 2020; 26 Graham (10.1016/j.celrep.2022.111276_bib19) 2021; 54 Hurt (10.1016/j.celrep.2022.111276_bib25) 2021; 13 Doores (10.1016/j.celrep.2022.111276_bib13) 2010; 84 Wrapp (10.1016/j.celrep.2022.111276_bib59) 2020; 367 Seow (10.1016/j.celrep.2022.111276_bib47) 2022; 39 Barnes (10.1016/j.celrep.2022.111276_bib3) 2020; 588 Winstone (10.1016/j.celrep.2022.111276_bib58) 2021; 95 Engen (10.1016/j.celrep.2022.111276_bib15) 2020; 45 Seow (10.1016/j.celrep.2022.111276_bib48) 2020; 5 ter Meulen (10.1016/j.celrep.2022.111276_bib53) 2006; 3 Lau (10.1016/j.celrep.2022.111276_bib29) 2021; 37 Zufferey (10.1016/j.celrep.2022.111276_bib66) 1997; 15 Punjani (10.1016/j.celrep.2022.111276_bib38) 2017; 14 Scheres (10.1016/j.celrep.2022.111276_bib45) 2012; 9 Aricescu (10.1016/j.celrep.2022.111276_bib2) 2006; 62 Benton (10.1016/j.celrep.2022.111276_bib4) 2021; 118 Castro Dopico (10.1016/j.celrep.2022.111276_bib8) 2022; 291 Kidmose (10.1016/j.celrep.2022.111276_bib26) 2019; 6 Cerutti (10.1016/j.celrep.2022.111276_bib9) 2021; 29 Grehan (10.1016/j.celrep.2022.111276_bib21) 2015; 2 Lan (10.1016/j.celrep.2022.111276_bib28) 2020; 581 Rosenthal (10.1016/j.celrep.2022.111276_bib43) 2003; 333 Greaney (10.1016/j.celrep.2022.111276_bib20) 2021; 29 Sanchez-Garcia (10.1016/j.celrep.2022.111276_bib44) 2021; 4 Zhang (10.1016/j.celrep.2022.111276_bib62) 2021; 372 Monin (10.1016/j.celrep.2022.111276_bib34) 2021; 22 Terwilliger (10.1016/j.celrep.2022.111276_bib54) 2020; 17 Rogers (10.1016/j.celrep.2022.111276_bib41) 2020; 369 Afonine (10.1016/j.celrep.2022.111276_bib1) 2018; 74 Zheng (10.1016/j.celrep.2022.111276_bib64) 2017; 14 Emsley (10.1016/j.celrep.2022.111276_bib14) 2004; 60 Benton (10.1016/j.celrep.2022.111276_bib5) 2020; 588 Krammer (10.1016/j.celrep.2022.111276_bib27) 2020; 586 Wrobel (10.1016/j.celrep.2022.111276_bib60) 2020; 27 Hurlburt (10.1016/j.celrep.2022.111276_bib24) 2020; 11 Brouwer (10.1016/j.celrep.2022.111276_bib6) 2020; 369 Dixon (10.1016/j.celrep.2022.111276_bib12) 2014 Tay (10.1016/j.celrep.2022.111276_bib51) 2020; 20 Huo (10.1016/j.celrep.2022.111276_bib23) 2021; 12
References_xml	– volume: 9 start-page: 853 year: 2012 end-page: 854 ident: bib45 article-title: Prevention of overfitting in cryo-EM structure determination publication-title: Nat. Methods – volume: 24 start-page: 3585 year: 2010 end-page: 3592 ident: bib10 article-title: Expansion of time window for mass spectrometric measurement of amide hydrogen/deuterium exchange reactions publication-title: Rapid Commun. Mass Spectrom. – volume: 6 start-page: 5 year: 2019 end-page: 17 ident: bib65 article-title: A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis publication-title: IUCrJ – volume: 118 year: 2021 ident: bib4 article-title: The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2 publication-title: Proc. Natl. Acad. Sci. USA – volume: 60 start-page: 2126 year: 2004 end-page: 2132 ident: bib14 article-title: Coot: model-building tools for molecular graphics publication-title: Acta Crystallogr. D Biol. Crystallogr. – volume: 20 start-page: 363 year: 2020 end-page: 374 ident: bib51 article-title: The trinity of COVID-19: immunity, inflammation and intervention publication-title: Nat. Rev. Immunol. – year: 2014 ident: bib12 article-title: Mechanisms of immunoglobulin deactivation by Streptococcus pyogenes publication-title: PhD Thesis – volume: 29 start-page: 463 year: 2021 end-page: 476.e6 ident: bib20 article-title: Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies publication-title: Cell Host Microbe – volume: 6 start-page: 526 year: 2019 end-page: 531 ident: bib26 article-title: Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps publication-title: IUCrJ – volume: 16 start-page: 595 year: 2019 end-page: 602 ident: bib31 article-title: Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments publication-title: Nat. Methods – volume: 586 start-page: 516 year: 2020 end-page: 527 ident: bib27 article-title: SARS-CoV-2 vaccines in development publication-title: Nature – volume: 41 start-page: 1006 year: 2020 end-page: 1022 ident: bib16 article-title: Structural basis of SARS-CoV-2 and SARS-CoV antibody interactions publication-title: Trends Immunol. – volume: 3 start-page: e237 year: 2006 ident: bib53 article-title: Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants publication-title: PLoS Med. – volume: 584 start-page: 437 year: 2020 end-page: 442 ident: bib40 article-title: Convergent antibody responses to SARS-CoV-2 in convalescent individuals publication-title: Nature – volume: 24 start-page: 1584 year: 2013 end-page: 1592 ident: bib18 article-title: Time window expansion for HDX analysis of an intrinsically disordered protein publication-title: J. Am. Soc. Mass Spectrom. – volume: 13 year: 2022 ident: bib30 article-title: Broad neutralization of SARS-CoV-2 variants, including omicron, following breakthrough infection with delta in COVID-19-vaccinated individuals publication-title: mBio – volume: 27 start-page: 293 year: 2018 end-page: 315 ident: bib57 article-title: MolProbity: more and better reference data for improved all-atom structure validation publication-title: Protein Sci. – volume: 293 start-page: 14678 year: 2018 end-page: 14688 ident: bib33 article-title: Agonistic beta-Klotho antibody mimics fibroblast growth factor 21 (FGF21) functions publication-title: J. Biol. Chem. – volume: 21 start-page: 382 year: 2021 end-page: 393 ident: bib52 article-title: Neutralizing monoclonal antibodies for treatment of COVID-19 publication-title: Nat. Rev. Immunol. – volume: 581 start-page: 215 year: 2020 end-page: 220 ident: bib28 article-title: Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor publication-title: Nature – volume: 17 start-page: 923 year: 2020 end-page: 927 ident: bib54 article-title: Improvement of cryo-EM maps by density modification publication-title: Nat. Methods – volume: 14 start-page: 290 year: 2017 end-page: 296 ident: bib38 article-title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination publication-title: Nat. Methods – volume: 14 start-page: 331 year: 2017 end-page: 332 ident: bib64 article-title: MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy publication-title: Nat. Methods – volume: 369 start-page: 643 year: 2020 end-page: 650 ident: bib6 article-title: Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability publication-title: Science – volume: 15 start-page: 871 year: 1997 end-page: 875 ident: bib66 article-title: Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo publication-title: Nat. Biotechnol. – volume: 38 year: 2022 ident: bib50 article-title: Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display publication-title: Cell Rep. – volume: 39 start-page: 110757 year: 2022 ident: bib47 article-title: ChAdOx1 nCoV-19 vaccine elicits monoclonal antibodies with cross-neutralizing activity against SARS-CoV-2 viral variants publication-title: Cell Rep. – volume: 84 start-page: 10510 year: 2010 end-page: 10521 ident: bib13 article-title: Variable loop glycan dependency of the broad and potent HIV-1-neutralizing antibodies PG9 and PG16 publication-title: J. Virol. – volume: 184 start-page: 4593 year: 2021 end-page: 4595 ident: bib11 article-title: Tackling COVID-19 with neutralizing monoclonal antibodies publication-title: Cell – volume: 37 start-page: 270 year: 2021 end-page: 272 ident: bib29 article-title: Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry publication-title: Bioinformatics – volume: 79 start-page: 1635 year: 2005 end-page: 1644 ident: bib56 article-title: Molecular and biological characterization of human monoclonal antibodies binding to the spike and nucleocapsid proteins of severe acute respiratory syndrome coronavirus publication-title: J. Virol. – volume: 291 start-page: 32 year: 2022 end-page: 50 ident: bib8 article-title: Immunity to SARS-CoV-2 induced by infection or vaccination publication-title: J. Intern. Med. – volume: 588 start-page: 682 year: 2020 end-page: 687 ident: bib3 article-title: SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies publication-title: Nature – volume: 1824 start-page: 520 year: 2012 end-page: 532 ident: bib39 article-title: Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures publication-title: Biochim. Biophys. Acta – volume: 95 year: 2021 ident: bib58 article-title: The polybasic cleavage site in the SARS-CoV-2 spike modulates viral sensitivity to Type I interferon and IFITM2 publication-title: J. Virol. – volume: 29 start-page: 819 year: 2021 end-page: 833.e7 ident: bib9 article-title: Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite publication-title: Cell Host Microbe – year: 2021 ident: bib32 article-title: N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2 publication-title: Cell – volume: 588 start-page: 327 year: 2020 end-page: 330 ident: bib5 article-title: Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion publication-title: Nature – volume: 25 year: 2020 ident: bib55 article-title: Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020 publication-title: Euro Surveill. – volume: 5 start-page: 1598 year: 2020 end-page: 1607 ident: bib48 article-title: Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans publication-title: Nat. Microbiol. – volume: 538 start-page: 192 year: 2021 end-page: 203 ident: bib61 article-title: Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies publication-title: Biochem. Biophys. Res. Commun. – volume: 14 start-page: 793 year: 2017 end-page: 796 ident: bib49 article-title: Addressing preferred specimen orientation in single-particle cryo-EM through tilting publication-title: Nat. Methods – volume: 369 start-page: 956 year: 2020 end-page: 963 ident: bib41 article-title: Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model publication-title: Science – volume: 333 start-page: 721 year: 2003 end-page: 745 ident: bib43 article-title: Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy publication-title: J. Mol. Biol. – volume: 13 start-page: 628 year: 2021 ident: bib25 article-title: Neutralizing antibody therapeutics for COVID-19 publication-title: Viruses – volume: 12 start-page: 5469 year: 2021 ident: bib23 article-title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19 publication-title: Nat. Commun. – volume: 27 start-page: 763 year: 2020 end-page: 767 ident: bib60 article-title: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects publication-title: Nat. Struct. Mol. Biol. – volume: 41 start-page: 1141 year: 2020 end-page: 1149 ident: bib22 article-title: Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 publication-title: Acta Pharmacol. Sin. – volume: 54 start-page: 1276 year: 2021 end-page: 1289.e6 ident: bib19 article-title: Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant publication-title: Immunity – volume: 2 start-page: 379 year: 2015 end-page: 384 ident: bib21 article-title: An optimised method for the production of MERS-CoV spike expressing viral pseudotypes publication-title: MethodsX – volume: 22 start-page: 765 year: 2021 end-page: 778 ident: bib34 article-title: Safety and immunogenicity of one versus two doses of the COVID-19 vaccine BNT162b2 for patients with cancer: interim analysis of a prospective observational study publication-title: Lancet Oncol. – volume: 183 start-page: 1024 year: 2020 end-page: 1042.e21 ident: bib36 article-title: Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology publication-title: Cell – volume: 25 start-page: 1605 year: 2004 end-page: 1612 ident: bib35 article-title: UCSF Chimera--a visualization system for exploratory research and analysis publication-title: J. Comput. Chem. – volume: 16 year: 2020 ident: bib37 article-title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings publication-title: PLoS Pathog. – volume: 373 start-page: eabi6226 year: 2021 ident: bib17 article-title: Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity publication-title: Science – volume: 74 start-page: 531 year: 2018 end-page: 544 ident: bib1 article-title: Real-space refinement in PHENIX for cryo-EM and crystallography publication-title: Acta Crystallogr. D Struct. Biol. – volume: 11 start-page: 5413 year: 2020 ident: bib24 article-title: Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation publication-title: Nat. Commun. – volume: 76 start-page: 94 year: 2020 end-page: 101 ident: bib46 article-title: Amyloid structure determination in RELION-3.1 publication-title: Acta Crystallogr. D Struct. Biol. – volume: 372 start-page: 525 year: 2021 end-page: 530 ident: bib62 article-title: Structural impact on SARS-CoV-2 spike protein by D614G substitution publication-title: Science – volume: 193 start-page: 1 year: 2016 end-page: 12 ident: bib63 article-title: Gctf: real-time CTF determination and correction publication-title: J. Struct. Biol. – volume: 7 year: 2021 ident: bib42 article-title: SARS-CoV-2 can recruit a haem metabolite to evade antibody immunity publication-title: Sci. Adv. – volume: 26 start-page: 1701 year: 2020 end-page: 1707 ident: bib7 article-title: Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection publication-title: Nat. Med. – volume: 45 start-page: 906 year: 2020 end-page: 918 ident: bib15 article-title: Complementarity of hydrogen/deuterium exchange mass spectrometry and cryo-electron microscopy publication-title: Trends Biochem. Sci. – volume: 367 start-page: 1260 year: 2020 end-page: 1263 ident: bib59 article-title: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation publication-title: Science – volume: 62 start-page: 1243 year: 2006 end-page: 1250 ident: bib2 article-title: A time- and cost-efficient system for high-level protein production in mammalian cells publication-title: Acta Crystallogr. D Biol. Crystallogr. – volume: 4 start-page: 874 year: 2021 ident: bib44 article-title: DeepEMhancer: a deep learning solution for cryo-EM volume post-processing publication-title: Commun. Biol. – volume: 25 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib55 article-title: Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020 publication-title: Euro Surveill. doi: 10.2807/1560-7917.ES.2020.25.42.2000685 – volume: 367 start-page: 1260 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib59 article-title: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation publication-title: Science doi: 10.1126/science.abb2507 – volume: 2 start-page: 379 year: 2015 ident: 10.1016/j.celrep.2022.111276_bib21 article-title: An optimised method for the production of MERS-CoV spike expressing viral pseudotypes publication-title: MethodsX doi: 10.1016/j.mex.2015.09.003 – volume: 1824 start-page: 520 year: 2012 ident: 10.1016/j.celrep.2022.111276_bib39 article-title: Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures publication-title: Biochim. Biophys. Acta doi: 10.1016/j.bbapap.2011.12.007 – volume: 79 start-page: 1635 year: 2005 ident: 10.1016/j.celrep.2022.111276_bib56 article-title: Molecular and biological characterization of human monoclonal antibodies binding to the spike and nucleocapsid proteins of severe acute respiratory syndrome coronavirus publication-title: J. Virol. doi: 10.1128/JVI.79.3.1635-1644.2005 – volume: 16 start-page: 595 year: 2019 ident: 10.1016/j.celrep.2022.111276_bib31 article-title: Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments publication-title: Nat. Methods doi: 10.1038/s41592-019-0459-y – volume: 4 start-page: 874 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib44 article-title: DeepEMhancer: a deep learning solution for cryo-EM volume post-processing publication-title: Commun. Biol. doi: 10.1038/s42003-021-02399-1 – volume: 538 start-page: 192 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib61 article-title: Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies publication-title: Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2020.10.012 – volume: 95 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib58 article-title: The polybasic cleavage site in the SARS-CoV-2 spike modulates viral sensitivity to Type I interferon and IFITM2 publication-title: J. Virol. doi: 10.1128/JVI.02422-20 – volume: 26 start-page: 1701 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib7 article-title: Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection publication-title: Nat. Med. doi: 10.1038/s41591-020-1054-6 – volume: 14 start-page: 290 year: 2017 ident: 10.1016/j.celrep.2022.111276_bib38 article-title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination publication-title: Nat. Methods doi: 10.1038/nmeth.4169 – volume: 74 start-page: 531 year: 2018 ident: 10.1016/j.celrep.2022.111276_bib1 article-title: Real-space refinement in PHENIX for cryo-EM and crystallography publication-title: Acta Crystallogr. D Struct. Biol. doi: 10.1107/S2059798318006551 – volume: 29 start-page: 463 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib20 article-title: Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.02.003 – volume: 118 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib4 article-title: The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2 publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.2022586118 – volume: 7 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib42 article-title: SARS-CoV-2 can recruit a haem metabolite to evade antibody immunity publication-title: Sci. Adv. doi: 10.1126/sciadv.abg7607 – volume: 16 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib37 article-title: Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings publication-title: PLoS Pathog. doi: 10.1371/journal.ppat.1008817 – volume: 586 start-page: 516 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib27 article-title: SARS-CoV-2 vaccines in development publication-title: Nature doi: 10.1038/s41586-020-2798-3 – volume: 37 start-page: 270 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib29 article-title: Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry publication-title: Bioinformatics doi: 10.1093/bioinformatics/btaa677 – volume: 372 start-page: 525 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib62 article-title: Structural impact on SARS-CoV-2 spike protein by D614G substitution publication-title: Science doi: 10.1126/science.abf2303 – volume: 29 start-page: 819 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib9 article-title: Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.03.005 – volume: 84 start-page: 10510 year: 2010 ident: 10.1016/j.celrep.2022.111276_bib13 article-title: Variable loop glycan dependency of the broad and potent HIV-1-neutralizing antibodies PG9 and PG16 publication-title: J. Virol. doi: 10.1128/JVI.00552-10 – volume: 291 start-page: 32 year: 2022 ident: 10.1016/j.celrep.2022.111276_bib8 article-title: Immunity to SARS-CoV-2 induced by infection or vaccination publication-title: J. Intern. Med. doi: 10.1111/joim.13372 – volume: 184 start-page: 4593 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib11 article-title: Tackling COVID-19 with neutralizing monoclonal antibodies publication-title: Cell doi: 10.1016/j.cell.2021.07.027 – volume: 20 start-page: 363 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib51 article-title: The trinity of COVID-19: immunity, inflammation and intervention publication-title: Nat. Rev. Immunol. doi: 10.1038/s41577-020-0311-8 – volume: 6 start-page: 5 year: 2019 ident: 10.1016/j.celrep.2022.111276_bib65 article-title: A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis publication-title: IUCrJ doi: 10.1107/S205225251801463X – year: 2014 ident: 10.1016/j.celrep.2022.111276_bib12 article-title: Mechanisms of immunoglobulin deactivation by Streptococcus pyogenes publication-title: PhD Thesis – volume: 13 year: 2022 ident: 10.1016/j.celrep.2022.111276_bib30 article-title: Broad neutralization of SARS-CoV-2 variants, including omicron, following breakthrough infection with delta in COVID-19-vaccinated individuals publication-title: mBio doi: 10.1128/mbio.03798-21 – volume: 11 start-page: 5413 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib24 article-title: Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation publication-title: Nat. Commun. doi: 10.1038/s41467-020-19231-9 – volume: 27 start-page: 763 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib60 article-title: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects publication-title: Nat. Struct. Mol. Biol. doi: 10.1038/s41594-020-0468-7 – volume: 333 start-page: 721 year: 2003 ident: 10.1016/j.celrep.2022.111276_bib43 article-title: Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2003.07.013 – volume: 369 start-page: 643 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib6 article-title: Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability publication-title: Science doi: 10.1126/science.abc5902 – volume: 12 start-page: 5469 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib23 article-title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19 publication-title: Nat. Commun. doi: 10.1038/s41467-021-25480-z – volume: 369 start-page: 956 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib41 article-title: Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model publication-title: Science doi: 10.1126/science.abc7520 – volume: 39 start-page: 110757 year: 2022 ident: 10.1016/j.celrep.2022.111276_bib47 article-title: ChAdOx1 nCoV-19 vaccine elicits monoclonal antibodies with cross-neutralizing activity against SARS-CoV-2 viral variants publication-title: Cell Rep. doi: 10.1016/j.celrep.2022.110757 – volume: 9 start-page: 853 year: 2012 ident: 10.1016/j.celrep.2022.111276_bib45 article-title: Prevention of overfitting in cryo-EM structure determination publication-title: Nat. Methods doi: 10.1038/nmeth.2115 – volume: 25 start-page: 1605 year: 2004 ident: 10.1016/j.celrep.2022.111276_bib35 article-title: UCSF Chimera--a visualization system for exploratory research and analysis publication-title: J. Comput. Chem. doi: 10.1002/jcc.20084 – volume: 588 start-page: 682 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib3 article-title: SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies publication-title: Nature doi: 10.1038/s41586-020-2852-1 – volume: 5 start-page: 1598 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib48 article-title: Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans publication-title: Nat. Microbiol. doi: 10.1038/s41564-020-00813-8 – volume: 17 start-page: 923 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib54 article-title: Improvement of cryo-EM maps by density modification publication-title: Nat. Methods doi: 10.1038/s41592-020-0914-9 – volume: 14 start-page: 793 year: 2017 ident: 10.1016/j.celrep.2022.111276_bib49 article-title: Addressing preferred specimen orientation in single-particle cryo-EM through tilting publication-title: Nat. Methods doi: 10.1038/nmeth.4347 – volume: 76 start-page: 94 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib46 article-title: Amyloid structure determination in RELION-3.1 publication-title: Acta Crystallogr. D Struct. Biol. doi: 10.1107/S2059798319016577 – volume: 14 start-page: 331 year: 2017 ident: 10.1016/j.celrep.2022.111276_bib64 article-title: MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy publication-title: Nat. Methods doi: 10.1038/nmeth.4193 – volume: 41 start-page: 1141 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib22 article-title: Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 publication-title: Acta Pharmacol. Sin. doi: 10.1038/s41401-020-0485-4 – volume: 584 start-page: 437 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib40 article-title: Convergent antibody responses to SARS-CoV-2 in convalescent individuals publication-title: Nature doi: 10.1038/s41586-020-2456-9 – volume: 27 start-page: 293 year: 2018 ident: 10.1016/j.celrep.2022.111276_bib57 article-title: MolProbity: more and better reference data for improved all-atom structure validation publication-title: Protein Sci. doi: 10.1002/pro.3330 – volume: 13 start-page: 628 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib25 article-title: Neutralizing antibody therapeutics for COVID-19 publication-title: Viruses doi: 10.3390/v13040628 – volume: 293 start-page: 14678 year: 2018 ident: 10.1016/j.celrep.2022.111276_bib33 article-title: Agonistic beta-Klotho antibody mimics fibroblast growth factor 21 (FGF21) functions publication-title: J. Biol. Chem. doi: 10.1074/jbc.RA118.004343 – volume: 6 start-page: 526 year: 2019 ident: 10.1016/j.celrep.2022.111276_bib26 article-title: Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps publication-title: IUCrJ doi: 10.1107/S2052252519007619 – volume: 24 start-page: 1584 year: 2013 ident: 10.1016/j.celrep.2022.111276_bib18 article-title: Time window expansion for HDX analysis of an intrinsically disordered protein publication-title: J. Am. Soc. Mass Spectrom. doi: 10.1007/s13361-013-0669-y – volume: 24 start-page: 3585 year: 2010 ident: 10.1016/j.celrep.2022.111276_bib10 article-title: Expansion of time window for mass spectrometric measurement of amide hydrogen/deuterium exchange reactions publication-title: Rapid Commun. Mass Spectrom. doi: 10.1002/rcm.4814 – volume: 54 start-page: 1276 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib19 article-title: Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant publication-title: Immunity doi: 10.1016/j.immuni.2021.03.023 – volume: 62 start-page: 1243 year: 2006 ident: 10.1016/j.celrep.2022.111276_bib2 article-title: A time- and cost-efficient system for high-level protein production in mammalian cells publication-title: Acta Crystallogr. D Biol. Crystallogr. doi: 10.1107/S0907444906029799 – year: 2021 ident: 10.1016/j.celrep.2022.111276_bib32 article-title: N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2 publication-title: Cell doi: 10.1016/j.cell.2021.03.028 – volume: 588 start-page: 327 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib5 article-title: Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion publication-title: Nature doi: 10.1038/s41586-020-2772-0 – volume: 193 start-page: 1 year: 2016 ident: 10.1016/j.celrep.2022.111276_bib63 article-title: Gctf: real-time CTF determination and correction publication-title: J. Struct. Biol. doi: 10.1016/j.jsb.2015.11.003 – volume: 581 start-page: 215 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib28 article-title: Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor publication-title: Nature doi: 10.1038/s41586-020-2180-5 – volume: 41 start-page: 1006 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib16 article-title: Structural basis of SARS-CoV-2 and SARS-CoV antibody interactions publication-title: Trends Immunol. doi: 10.1016/j.it.2020.09.004 – volume: 60 start-page: 2126 year: 2004 ident: 10.1016/j.celrep.2022.111276_bib14 article-title: Coot: model-building tools for molecular graphics publication-title: Acta Crystallogr. D Biol. Crystallogr. doi: 10.1107/S0907444904019158 – volume: 22 start-page: 765 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib34 article-title: Safety and immunogenicity of one versus two doses of the COVID-19 vaccine BNT162b2 for patients with cancer: interim analysis of a prospective observational study publication-title: Lancet Oncol. doi: 10.1016/S1470-2045(21)00213-8 – volume: 45 start-page: 906 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib15 article-title: Complementarity of hydrogen/deuterium exchange mass spectrometry and cryo-electron microscopy publication-title: Trends Biochem. Sci. doi: 10.1016/j.tibs.2020.05.005 – volume: 15 start-page: 871 year: 1997 ident: 10.1016/j.celrep.2022.111276_bib66 article-title: Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo publication-title: Nat. Biotechnol. doi: 10.1038/nbt0997-871 – volume: 183 start-page: 1024 year: 2020 ident: 10.1016/j.celrep.2022.111276_bib36 article-title: Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology publication-title: Cell doi: 10.1016/j.cell.2020.09.037 – volume: 38 year: 2022 ident: 10.1016/j.celrep.2022.111276_bib50 article-title: Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display publication-title: Cell Rep. doi: 10.1016/j.celrep.2022.110348 – volume: 21 start-page: 382 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib52 article-title: Neutralizing monoclonal antibodies for treatment of COVID-19 publication-title: Nat. Rev. Immunol. doi: 10.1038/s41577-021-00542-x – volume: 3 start-page: e237 year: 2006 ident: 10.1016/j.celrep.2022.111276_bib53 article-title: Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants publication-title: PLoS Med. doi: 10.1371/journal.pmed.0030237 – volume: 373 start-page: eabi6226 year: 2021 ident: 10.1016/j.celrep.2022.111276_bib17 article-title: Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity publication-title: Science doi: 10.1126/science.abi6226
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Snippet	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination....
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SubjectTerms	Antibodies, Neutralizing Antibodies, Viral antibody COVID-19 Cryoelectron Microscopy cryogenic electron microscopy Epitopes Humans hydrogen-deuterium exchange Neutralization Tests neutralizing epitope omicron SARS-CoV-2 Spike Glycoprotein, Coronavirus spike subdomain 1 Syndactyly Vaccination
Title	A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination
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