Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single s

Cerutti, Gabriele; Guo, Yicheng; Zhou, Tongqing; Gorman, Jason; Lee, Myungjin; Rapp, Micah; Reddem, Eswar R.; Yu, Jian; Bahna, Fabiana; Bimela, Jude; Huang, Yaoxing; Katsamba, Phinikoula S.; Liu, Lihong; Nair, Manoj S.; Rawi, Reda; Olia, Adam S.; Wang, Pengfei; Zhang, Baoshan; Chuang, Gwo-Yu; Ho, David D.; Sheng, Zizhang; Kwong, Peter D.; Shapiro, Lawrence

doi:10.1016/j.chom.2021.03.005

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single s

Journal Article · 01 May 2021 · Cell Host Microbe

DOI:https://doi.org/10.1016/j.chom.2021.03.005· OSTI ID:1786007

Cerutti, Gabriele; Guo, Yicheng; Zhou, Tongqing; Gorman, Jason; Lee, Myungjin; Rapp, Micah; Reddem, Eswar R.; Yu, Jian; Bahna, Fabiana; Bimela, Jude; Huang, Yaoxing; Katsamba, Phinikoula S.; Liu, Lihong; Nair, Manoj S.; Rawi, Reda; Olia, Adam S.; Wang, Pengfei; Zhang, Baoshan; Chuang, Gwo-Yu; Ho, David D. more »

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1786007

Journal Information:: Cell Host Microbe, Vol. 29, Issue (5)

Country of Publication:: United States

Language:: ENGLISH

References (75)

Recent developments in the PHENIX software for automated crystallographic structure determination Adams, Paul D.; Gopal, Kreshna; Grosse-Kunstleve, Ralf W. Journal of Synchrotron Radiation, Vol. 11, Issue 1 https://doi.org/10.1107/S0909049503024130	journal	November 2003
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3541	journal	August 2015
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies Barnes, Christopher O.; Jette, Claudia A.; Abernathy, Morgan E. Nature, Vol. 588, Issue 7839 https://doi.org/10.1038/s41586-020-2852-1	journal	October 2020
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies Barnes, Christopher O.; West, Anthony P.; Huey-Tubman, Kathryn E. Cell, Vol. 182, Issue 4 https://doi.org/10.1016/j.cell.2020.06.025	journal	August 2020
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion Benton, Donald J.; Wrobel, Antoni G.; Xu, Pengqi Nature, Vol. 588, Issue 7837 https://doi.org/10.1038/s41586-020-2772-0	journal	September 2020
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs Bepler, Tristan; Morin, Andrew; Rapp, Micah Nature Methods, Vol. 16, Issue 11 https://doi.org/10.1038/s41592-019-0575-8	journal	October 2019
IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis Brochet, X.; Lefranc, M. -P.; Giudicelli, V. Nucleic Acids Research, Vol. 36, Issue Web Server https://doi.org/10.1093/nar/gkn316	journal	May 2008
Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability Brouwer, Philip J. M.; Caniels, Tom G.; van der Straten, Karlijn Science, Vol. 369, Issue 6504 https://doi.org/10.1126/science.abc5902	journal	June 2020
Rational Vaccine Design in the Time of COVID-19 Burton, Dennis R.; Walker, Laura M. Cell Host & Microbe, Vol. 27, Issue 5 https://doi.org/10.1016/j.chom.2020.04.022	journal	May 2020
The coronavirus pandemic in five powerful charts Callaway, Ewen; Cyranoski, David; Mallapaty, Smriti Nature, Vol. 579, Issue 7800 https://doi.org/10.1038/d41586-020-00758-2	journal	March 2020
Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells Cao, Yunlong; Su, Bin; Guo, Xianghua Cell, Vol. 182, Issue 1 https://doi.org/10.1016/j.cell.2020.05.025	journal	July 2020
Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein Casalino, Lorenzo; Gaieb, Zied; Goldsmith, Jory A. ACS Central Science, Vol. 6, Issue 10 https://doi.org/10.1021/acscentsci.0c01056	journal	September 2020
A novel neutralizing monoclonal antibody targeting the N-terminal domain of the MERS-CoV spike protein Chen, Yingzhu; Lu, Shuai; Jia, Hao Emerging Microbes & Infections, Vol. 6, Issue 1 https://doi.org/10.1038/emi.2017.50	journal	January 2017
Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor Chen, Xiangyu; Li, Ren; Pan, Zhiwei Cellular & Molecular Immunology, Vol. 17, Issue 6 https://doi.org/10.1038/s41423-020-0426-7	journal	April 2020
A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Chi, Xiangyang; Yan, Renhong; Zhang, Jun Science, Vol. 369, Issue 6504 https://doi.org/10.1126/science.abc6952	journal	June 2020
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Davis, I. W.; Murray, L. W.; Richardson, J. S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh398	journal	July 2004
An interactive web-based dashboard to track COVID-19 in real time Dong, Ensheng; Du, Hongru; Gardner, Lauren The Lancet Infectious Diseases, Vol. 20, Issue 5 https://doi.org/10.1016/S1473-3099(20)30120-1	journal	May 2020
SAbPred: a structure-based antibody prediction server Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw361	journal	April 2016
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Bio3d: an R package for the comparative analysis of protein structures Grant, B. J.; Rodrigues, A. P. C.; ElSawy, K. M. Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl461	journal	August 2006
Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail Hansen, Johanna; Baum, Alina; Pascal, Kristen E. Science https://doi.org/10.1126/science.abd0827	journal	June 2020
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes Hsieh, Ching-Lin; Goldsmith, Jory A.; Schaub, Jeffrey M. Science, Vol. 369, Issue 6510 https://doi.org/10.1126/science.abd0826	journal	July 2020
CHARMM-GUI: A web-based graphical user interface for CHARMM Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G. Journal of Computational Chemistry, Vol. 29, Issue 11 https://doi.org/10.1002/jcc.20945	journal	March 2008
The PDB_REDO server for macromolecular structure model optimization Joosten, Robbie P.; Long, Fei; Murshudov, Garib N. IUCrJ, Vol. 1, Issue 4 https://doi.org/10.1107/S2052252514009324	journal	May 2014
Human neutralizing antibodies elicited by SARS-CoV-2 infection Ju, Bin; Zhang, Qi; Ge, Jiwan Nature, Vol. 584, Issue 7819 https://doi.org/10.1038/s41586-020-2380-z	journal	May 2020
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Katoh, K. Nucleic Acids Research, Vol. 30, Issue 14 https://doi.org/10.1093/nar/gkf436	journal	July 2002
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120 Kong, Leopold; Lee, Jeong Hyun; Doores, Katie J. Nature Structural & Molecular Biology, Vol. 20, Issue 7 https://doi.org/10.1038/nsmb.2594	journal	May 2013
Longitudinal Isolation of Potent Near-Germline SARS-CoV-2-Neutralizing Antibodies from COVID-19 Patients Kreer, Christoph; Zehner, Matthias; Weber, Timm Cell, Vol. 182, Issue 6 https://doi.org/10.1016/j.cell.2020.08.046	journal	September 2020
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
A V _H 1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite Kumar, Sonu; Ju, Bin; Shapero, Benjamin Science Advances, Vol. 6, Issue 38 https://doi.org/10.1126/sciadv.abb1328	journal	September 2020
IMGT®, the International ImMunoGeneTics Information System® for Immunoinformatics: Methods for Querying IMGT® Databases, Tools, and Web Resources in the Context of Immunoinformatics Lefranc, Marie-Paule Molecular Biotechnology, Vol. 40, Issue 1 https://doi.org/10.1007/s12033-008-9062-7	journal	May 2008
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike Liu, Lihong; Wang, Pengfei; Nair, Manoj S. Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2571-7	journal	July 2020
Multiple Antibody Lineages in One Donor Target the Glycan-V3 Supersite of the HIV-1 Envelope Glycoprotein and Display a Preference for Quaternary Binding Longo, Nancy S.; Sutton, Matthew S.; Shiakolas, Andrea R. Journal of Virology, Vol. 90, Issue 23 https://doi.org/10.1128/JVI.01012-16	journal	September 2016
Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody Lv, Zhe; Deng, Yong-Qiang; Ye, Qing Science, Vol. 369, Issue 6510 https://doi.org/10.1126/science.abc5881	journal	July 2020
Solving structures of protein complexes by molecular replacement with Phaser McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1 https://doi.org/10.1107/S0907444906045975	journal	December 2006
FreeSASA: An open source C library for solvent accessible surface area calculations Mitternacht, Simon F1000Research, Vol. 5 https://doi.org/10.12688/f1000research.7931.1	journal	January 2016
Targeting the N332-supersite of the HIV-1 envelope for vaccine design Moyo, Thandeka; Kitchin, Dale; Moore, Penny L. Expert Opinion on Therapeutic Targets, Vol. 24, Issue 6 https://doi.org/10.1080/14728222.2020.1752183	journal	April 2020
Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S. Proceedings of the National Academy of Sciences, Vol. 114, Issue 35 https://doi.org/10.1073/pnas.1707304114	journal	August 2017
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Pinto, Dora; Park, Young-Jun; Beltramello, Martina Nature, Vol. 583, Issue 7815 https://doi.org/10.1038/s41586-020-2349-y	journal	May 2020
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
Convergent antibody responses to SARS-CoV-2 in convalescent individuals Robbiani, Davide F.; Gaebler, Christian; Muecksch, Frauke Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2456-9	journal	June 2020
Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model Rogers, Thomas F.; Zhao, Fangzhu; Huang, Deli Science, Vol. 369, Issue 6506 https://doi.org/10.1126/science.abc7520	journal	June 2020
RELION: Implementation of a Bayesian approach to cryo-EM structure determination Scheres, Sjors H. W. Journal of Structural Biology, Vol. 180, Issue 3, p. 519-530 https://doi.org/10.1016/j.jsb.2012.09.006	journal	December 2012
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts Schramm, Chaim A.; Sheng, Zizhang; Zhang, Zhenhai Frontiers in Immunology, Vol. 7 https://doi.org/10.3389/fimmu.2016.00372	journal	September 2016
The Structural Basis of Antibody-Antigen Recognition Sela-Culang, Inbal; Kunik, Vered; Ofran, Yanay Frontiers in Immunology, Vol. 4 https://doi.org/10.3389/fimmu.2013.00302	journal	January 2013
Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation Sheng, Zizhang; Schramm, Chaim A.; Kong, Rui Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00537	journal	May 2017
Automated molecular microscopy: The new Leginon system Suloway, Christian; Pulokas, James; Fellmann, Denis Journal of Structural Biology, Vol. 151, Issue 1 https://doi.org/10.1016/j.jsb.2005.03.010	journal	July 2005
Addressing preferred specimen orientation in single-particle cryo-EM through tilting Tan, Yong Zi; Baldwin, Philip R.; Davis, Joseph H. Nature Methods, Vol. 14, Issue 8 https://doi.org/10.1038/nmeth.4347	journal	July 2017
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra Cell, Vol. 181, Issue 2 https://doi.org/10.1016/j.cell.2020.02.058	journal	April 2020
Importance of Neutralizing Monoclonal Antibodies Targeting Multiple Antigenic Sites on the Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein To Avoid Neutralization Escape Wang, Lingshu; Shi, Wei; Chappell, James D. Journal of Virology, Vol. 92, Issue 10 https://doi.org/10.1128/JVI.02002-17	journal	March 2018
A human monoclonal antibody blocking SARS-CoV-2 infection Wang, Chunyan; Li, Wentao; Drabek, Dubravka Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16256-y	journal	May 2020
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 Wang, Qihui; Zhang, Yanfang; Wu, Lili Cell, Vol. 181, Issue 4 https://doi.org/10.1016/j.cell.2020.03.045	journal	May 2020
Structure-based development of human antibody cocktails against SARS-CoV-2 Wang, Nan; Sun, Yao; Feng, Rui Cell Research, Vol. 31, Issue 1 https://doi.org/10.1038/s41422-020-00446-w	journal	December 2020
SWISS-MODEL: homology modelling of protein structures and complexes Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky427	journal	May 2018
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies Wrapp, Daniel; De Vlieger, Dorien; Corbett, Kizzmekia S. Cell, Vol. 181, Issue 5 https://doi.org/10.1016/j.cell.2020.04.031	journal	May 2020
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S. Science, Vol. 367, Issue 6483 https://doi.org/10.1126/science.abb2507	journal	February 2020
SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects Wrobel, Antoni G.; Benton, Donald J.; Xu, Pengqi Nature Structural & Molecular Biology, Vol. 27, Issue 8 https://doi.org/10.1038/s41594-020-0468-7	journal	July 2020
A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2 Wu, Yan; Wang, Feiran; Shen, Chenguang Science, Vol. 368, Issue 6496 https://doi.org/10.1126/science.abc2241	journal	May 2020
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Yan, Renhong; Zhang, Yuanyuan; Li, Yaning Science, Vol. 367, Issue 6485 https://doi.org/10.1126/science.abb2762	journal	March 2020
IgBLAST: an immunoglobulin variable domain sequence analysis tool Ye, Jian; Ma, Ning; Madden, Thomas L. Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt382	journal	May 2013
Structural basis of a shared antibody response to SARS-CoV-2 Yuan, Meng; Liu, Hejun; Wu, Nicholas C. Science, Vol. 369, Issue 6507 https://doi.org/10.1126/science.abd2321	journal	July 2020
A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV Yuan, Meng; Wu, Nicholas C.; Zhu, Xueyong Science, Vol. 368, Issue 6491 https://doi.org/10.1126/science.abb7269	journal	April 2020
Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy Zeng, Xin; Li, Lingfang; Lin, Jing Antibody Therapeutics, Vol. 3, Issue 2 https://doi.org/10.1093/abt/tbaa008	journal	April 2020
Transplanting Supersites of HIV-1 Vulnerability Zhou, Tongqing; Zhu, Jiang; Yang, Yongping PLoS ONE, Vol. 9, Issue 7 https://doi.org/10.1371/journal.pone.0099881	journal	July 2014
Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors Zhou, Tongqing; Lynch, Rebecca M.; Chen, Lei Cell, Vol. 161, Issue 6 https://doi.org/10.1016/j.cell.2015.05.007	journal	June 2015
Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein Zhou, Haixia; Chen, Yingzhu; Zhang, Shuyuan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10897-4	journal	July 2019
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains Zhou, Tongqing; Tsybovsky, Yaroslav; Gorman, Jason Cell Host & Microbe, Vol. 28, Issue 6 https://doi.org/10.1016/j.chom.2020.11.004	journal	December 2020
Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein Zost, Seth J.; Gilchuk, Pavlo; Chen, Rita E. Nature Medicine, Vol. 26, Issue 9 https://doi.org/10.1038/s41591-020-0998-x	journal	July 2020

Similar Records

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Journal Article · 2022 · mBio (Online) · OSTI ID:1982983

Altomare, Clara G.; Adelsberg, Daniel C.; Carreno, Juan Manuel; +6 more

A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice

Journal Article · 2021 · ACS Central Science · OSTI ID:1778237

Powell, Abigail E.; Zhang, Kaiming; Sanyal, Mrinmoy; +7 more

Broadening a SARS-CoV-1–neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution

Journal Article · 2023 · Science Signaling · OSTI ID:2423886

Zhao, Fangzhu; Yuan, Meng; Keating, Celina; +19 more

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single s

Citation Formats

References (75)

Similar Records

Related Subjects