7YCN

Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab

Summary for 7YCN

• Entry DOI: 10.2210/pdb7ycn/pdb
• Descriptor: Spike protein S1, IY-2A Fab heavy chain, IY-2A Fab light chain, ... (4 entities in total)
• Functional Keywords: antibody, sars-cov-2, spike, rbd, class 4, viral protein-immune system complex, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV,SARS-CoV-2); More
• Total number of polymer chains: 12
• Total formula weight: 276425.84

Authors

Mohapatra, A.,Chen, X. (deposition date: 2022-07-01, release date: 2023-02-01, Last modification date: 2024-11-20)

Primary citation

Huang, K.A.,Chen, X.,Mohapatra, A.,Nguyen, H.T.V.,Schimanski, L.,Tan, T.K.,Rijal, P.,Vester, S.K.,Hills, R.A.,Howarth, M.,Keeffe, J.R.,Cohen, A.A.,Kakutani, L.M.,Wu, Y.M.,Shahed-Al-Mahmud, M.,Chou, Y.C.,Bjorkman, P.J.,Townsend, A.R.,Ma, C.
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14:311-311, 2023

PubMed 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.

PubMed: 36658148
DOI: 10.1038/s41467-023-35949-8

Experimental method

X-RAY DIFFRACTION (2.85 Å)