7VYR

Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment

Summary for 7VYR

• Entry DOI: 10.2210/pdb7vyr/pdb
• Descriptor: D27 heavy chain, D27 light chain, Spike protein S1, ... (4 entities in total)
• Functional Keywords: computational design, neutralizing antibody, sars-cov-2, viral protein, immune system, viral protein-immune system complex, viral protein/immune system
• Biological source: Homo sapiens; More
• Total number of polymer chains: 6
• Total formula weight: 164850.67

Authors

Jeong, B.-S.,Oh, B.-H. (deposition date: 2021-11-15, release date: 2022-03-02, Last modification date: 2024-10-16)

Primary citation

Jeong, B.S.,Cha, J.S.,Hwang, I.,Kim, U.,Adolf-Bryfogle, J.,Coventry, B.,Cho, H.S.,Kim, K.D.,Oh, B.H.
Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants.
Mabs, 14:2021601-2021601, 2022

PubMed Abstract: Coronavirus disease 2019, caused by SARS-CoV-2, remains an on-going pandemic, partly due to the emergence of variant viruses that can "break-through" the protection of the current vaccines and neutralizing antibodies (nAbs), highlighting the needs for broadly nAbs and next-generation vaccines. We report an antibody that exhibits breadth and potency in binding the receptor-binding domain (RBD) of the virus spike glycoprotein across SARS coronaviruses. Initially, a lead antibody was computationally discovered and crystallographically validated that binds to a highly conserved surface of the RBD of wild-type SARS-CoV-2. Subsequently, through experimental affinity enhancement and computational affinity maturation, it was further developed to bind the RBD of all concerning SARS-CoV-2 variants, SARS-CoV-1 and pangolin coronavirus with pico-molar binding affinities, consistently exhibited strong neutralization activity against wild-type SARS-CoV-2 and the Alpha and Delta variants. These results identify a vulnerable target site on coronaviruses for development of pan-sarbecovirus nAbs and vaccines.

PubMed: 35030983
DOI: 10.1080/19420862.2021.2021601

Experimental method

X-RAY DIFFRACTION (2.2 Å)