7JMO

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-04

Summary for 7JMO

• Entry DOI: 10.2210/pdb7jmo/pdb
• Descriptor: Spike protein S1, COVA2-04 heavy chain, COVA2-04 light chain, ... (5 entities in total)
• Functional Keywords: sars-cov-2, covid-19, rbd, antibody, sars, spike, immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV); More
• Total number of polymer chains: 3
• Total formula weight: 73813.49

Authors

Wu, N.C.,Yuan, M.,Liu, H.,Zhu, X.,Wilson, I.A. (deposition date: 2020-08-02, release date: 2020-08-26, Last modification date: 2024-11-06)

Primary citation

Wu, N.C.,Yuan, M.,Liu, H.,Lee, C.D.,Zhu, X.,Bangaru, S.,Torres, J.L.,Caniels, T.G.,Brouwer, P.J.M.,van Gils, M.J.,Sanders, R.W.,Ward, A.B.,Wilson, I.A.
An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Cell Rep, 33:108274-108274, 2020

PubMed Abstract: IGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 because of structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.

PubMed: 33027617
DOI: 10.1016/j.celrep.2020.108274

Experimental method

X-RAY DIFFRACTION (2.359 Å)