Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite
Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. He...
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| Published in | Cell host & microbe Vol. 29; no. 5; pp. 819 - 833.e7 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
12.05.2021
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site—formed primarily by a mobile β-hairpin and several flexible loops—was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.
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•Structures of seven NTD-directed neutralizing antibody complexes with spike or NTD•Structures define distinct recognition classes, one observed in multiple donors•Supersite is glycan free, electropositive, with mobile β-hairpin and flexible loops•Most potent NTD-directed neutralizing antibodies may target this supersite
Cerutti et al. report structural analysis of seven potent neutralizing antibodies targeting the N-terminal domain of SARS-CoV-2 spike. All antibodies recognize a common glycan-free, electropositive surface comprised of a mobile β-hairpin and flexible loops. While RBD-directed antibodies recognize non-overlapping epitopes, these findings indicate that NTD-directed antibodies predominantly target a single supersite. |
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| AbstractList | Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site—formed primarily by a mobile β-hairpin and several flexible loops—was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.
[Display omitted]
•Structures of seven NTD-directed neutralizing antibody complexes with spike or NTD•Structures define distinct recognition classes, one observed in multiple donors•Supersite is glycan free, electropositive, with mobile β-hairpin and flexible loops•Most potent NTD-directed neutralizing antibodies may target this supersite
Cerutti et al. report structural analysis of seven potent neutralizing antibodies targeting the N-terminal domain of SARS-CoV-2 spike. All antibodies recognize a common glycan-free, electropositive surface comprised of a mobile β-hairpin and flexible loops. While RBD-directed antibodies recognize non-overlapping epitopes, these findings indicate that NTD-directed antibodies predominantly target a single supersite. Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite. Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite. Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N 17, N 74, N 122, and N 149. This site—formed primarily by a mobile β-hairpin and several flexible loops—was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite. Cerutti et al. report structural analysis of seven potent neutralizing antibodies targeting the N-terminal domain of SARS-CoV-2 spike. All antibodies recognize a common glycan-free, electropositive surface comprised of a mobile β-hairpin and flexible loops. While RBD-directed antibodies recognize non-overlapping epitopes, these findings indicate that NTD-directed antibodies predominantly target a single supersite. |
| Author | Gorman, Jason Yu, Jian Bimela, Jude Huang, Yaoxing Zhang, Baoshan Nair, Manoj S. Liu, Lihong Rawi, Reda Reddem, Eswar R. Olia, Adam S. Kwong, Peter D. Rapp, Micah Chuang, Gwo-Yu Guo, Yicheng Bahna, Fabiana Katsamba, Phinikoula S. Zhou, Tongqing Cerutti, Gabriele Sheng, Zizhang Ho, David D. Lee, Myungjin Shapiro, Lawrence Wang, Pengfei |
| Author_xml | – sequence: 1 givenname: Gabriele surname: Cerutti fullname: Cerutti, Gabriele organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 2 givenname: Yicheng surname: Guo fullname: Guo, Yicheng organization: Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA – sequence: 3 givenname: Tongqing surname: Zhou fullname: Zhou, Tongqing organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 4 givenname: Jason surname: Gorman fullname: Gorman, Jason organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 5 givenname: Myungjin surname: Lee fullname: Lee, Myungjin organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 6 givenname: Micah surname: Rapp fullname: Rapp, Micah organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 7 givenname: Eswar R. surname: Reddem fullname: Reddem, Eswar R. organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 8 givenname: Jian surname: Yu fullname: Yu, Jian organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 9 givenname: Fabiana surname: Bahna fullname: Bahna, Fabiana organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 10 givenname: Jude surname: Bimela fullname: Bimela, Jude organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 11 givenname: Yaoxing surname: Huang fullname: Huang, Yaoxing organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 12 givenname: Phinikoula S. surname: Katsamba fullname: Katsamba, Phinikoula S. organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 13 givenname: Lihong surname: Liu fullname: Liu, Lihong organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 14 givenname: Manoj S. surname: Nair fullname: Nair, Manoj S. organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 15 givenname: Reda surname: Rawi fullname: Rawi, Reda organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 16 givenname: Adam S. surname: Olia fullname: Olia, Adam S. organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 17 givenname: Pengfei surname: Wang fullname: Wang, Pengfei organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 18 givenname: Baoshan surname: Zhang fullname: Zhang, Baoshan organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 19 givenname: Gwo-Yu surname: Chuang fullname: Chuang, Gwo-Yu organization: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA – sequence: 20 givenname: David D. surname: Ho fullname: Ho, David D. organization: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA – sequence: 21 givenname: Zizhang surname: Sheng fullname: Sheng, Zizhang organization: Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA – sequence: 22 givenname: Peter D. surname: Kwong fullname: Kwong, Peter D. email: pdkwong@nih.gov organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA – sequence: 23 givenname: Lawrence surname: Shapiro fullname: Shapiro, Lawrence email: lss8@columbia.edu organization: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33789084$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Antibodies, Neutralizing - chemistry Antibodies, Neutralizing - immunology Antibodies, Viral - chemistry Antibodies, Viral - immunology antibody class antigenic supersite COVID-19 Humans multi-donor antibody Mutation N-terminal domain neutralizing antibody Protein Conformation Protein Domains SARS-CoV-2 SARS-CoV-2 - immunology Spike Glycoprotein, Coronavirus - chemistry Spike Glycoprotein, Coronavirus - immunology |
| Title | Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite |
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