Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2

Creators: Huang, Kuan-Ying A.; Chen, Xiaorui; Mohapatra, Arpita; Nguyen, Hong Thuy Vy; Schimanski, Lisa; Tan, Tiong Kit; Rijal, Pramila; Vester, Susan K.; Hills, Rory A.; Howarth, Mark; Keeffe, Jennifer R.; Cohen, Alexander A.; Kakutani, Leesa M.; Wu, Yi-Min; Shahed-Al-Mahmud, Md; Chou, Yu-Chi; Bjorkman, Pamela J.; Townsend, Alain R.; Ma, Che

Abstract

Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.

Additional Information

© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. We acknowledge the BD FACSAria cell sorter service provided by the Core Instrument Center of Chang Gung University, Taiwan. We thank National RNAi Core Facility at Academia Sinica, Taiwan for pseudovirus neutralization assays. We thank the technical support provided by the National Synchrotron Radiation Research Center (NSRRC), Taiwan. We thank the Academia Sinica Biological Electron Microscopy Core Facility for negative stain EM and Academia Sinica Cryo-EM Facility (ASCEM) for cryo-EM support. We appreciate the advice from Dr. Shu-Chuan Jao for biolayer interferometry. The mutant BtKY72 was a kind gift from Alexandra Walls and David Veesler, University of Washington. This work was supported by the National Science and Technology Council of Taiwan (MOST 110-2628-B-182-009, MOST 110-2628-B-182-013, NTSC 111-2628-B-002-052) to K.-Y.A.H. The research was funded by Genomics Research Center, Summit Project (AS-SUMMIT-109) and the Translational Medical Research Program (AS-KPQ-109-BioMed), Academia Sinica, and Taiwan Bio-Development Foundation, to C.M. S.K.V. and M.H. were funded by the Biotechnology and Biological Sciences Research Council (BBSRC grant BB/T004983/1). P.J.B. was funded by Bill and Melinda Gates Foundation INV-034638, Caltech Merkin Institute, and George Mason University Fast Grant. R.A.H. was funded by the Rhodes Trust. M.H. also thanks the University of Oxford COVID-19 Research Response Fund and its donors (reference 0009517). The EM Facilities were funded by Academia Sinica Core Facility and Innovative Instrument Projects (AS-CFII-108-110 and AS-CFII-108-119) and Taiwan Protein Project (AS-KPQ-109-TPP2). This research was funded in whole or in part by BBSRC grant BB/T004983/1. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Data availability: The data associated with this study are available within the article, its supplementary information and Source Data file. Source data are provided with this paper. The coordinates and structure factors of the SARS-CoV-2 RBD/FP-12A, RBD/IS-9A and RBD/IY-2A crystallographic complexes generated in this study have been deposited in the PDB (Protein Data Bank) under accession codes 8HHF, 8HHG and 8HHH, respectively. Cryo-EM volumes and structure models of the SARS-CoV-2 Delta Spike/FP-12A, Delta Spike/IS-9A and BA.1 Spike/IY-2A generated in this study have been deposited in the EMDB (Electron Microscopy Data Bank) under accession codes EMD 34806, EMD 34807, and EMD 34808, and in the PDB under accession codes 8HHX, 8HHY and 8HHZ, respectively. Source data are provided with this paper. These authors contributed equally: Kuan-Ying A. Huang, Xiaorui Chen. Contributions: K.-Y.A.H. conceived and designed the study. K.-Y.A.H. isolated and characterized antibodies. L.S., T.K.T., P.R., and A.R.T. performed binding experiments and analyzed data. C.M. and X.C. supervised the structural study of antibodies. Y.C.C. performed SARS-CoV-2 variant neutralization experiments. S.K.V., R.A.H., and M.H. performed sarbecovirus RBD binding experiments and analyzed data. J.R.K., A.A.C., L.M.K., and P.J.B. performed sarbecovirus neutralization experiments and analyzed data. A.M. and H.T.V.N. determined crystal structures. A.M., X.C., Y.-M.W., and M.S-A.-M. performed cryo-EM grid preparation, data processing and structure refinement. K.-Y.A.H. and X.C. analyzed data and prepared figures and tables. K.-Y.A.H. and X.C. wrote the first draft of the manuscript. All authors read and approved the manuscript. The authors declare no competing interests.

Attached Files

Published - s41467-023-35949-8.pdf

Supplemental Material - s41467-023-35949-8MOESM1-ESM.pdf

Supplemental Material - s41467-023-35949-8MOESM3-ESM.xlsx

Files

s41467-023-35949-8.pdf

Files (18.4 MB)

Name	Size	Download all
s41467-023-35949-8MOESM3-ESM.xlsx md5:99749542268a9b6f8d6989828e182f38	31.6 kB	Download
s41467-023-35949-8MOESM1-ESM.pdf md5:a2a3ba32ba887909d715de5606789ad5	15.7 MB	Preview Download
s41467-023-35949-8.pdf md5:6926b1bb24f0dca472c56cee31ab7757	2.8 MB	Preview Download

Additional details

	All versions	This version
Views	0	0
Downloads	0	0
Data volume	0 Bytes	0 Bytes