7CH5

Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab

Summary for 7CH5

• Entry DOI: 10.2210/pdb7ch5/pdb
• Descriptor: BD-629 Fab H, BD-629 Fab L, Spike protein S1 (3 entities in total)
• Functional Keywords: complex, protein binding-immune system complex, protein binding/immune system
• Biological source: Homo sapiens; More
• Total number of polymer chains: 3
• Total formula weight: 72170.70

Authors

Du, S.,Xiao, J.Y. (deposition date: 2020-07-05, release date: 2020-09-16, Last modification date: 2023-11-29)

Primary citation

Du, S.,Cao, Y.,Zhu, Q.,Yu, P.,Qi, F.,Wang, G.,Du, X.,Bao, L.,Deng, W.,Zhu, H.,Liu, J.,Nie, J.,Zheng, Y.,Liang, H.,Liu, R.,Gong, S.,Xu, H.,Yisimayi, A.,Lv, Q.,Wang, B.,He, R.,Han, Y.,Zhao, W.,Bai, Y.,Qu, Y.,Gao, X.,Ji, C.,Wang, Q.,Gao, N.,Huang, W.,Wang, Y.,Xie, X.S.,Su, X.D.,Xiao, J.,Qin, C.
Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183:1013-1023.e13, 2020

PubMed Abstract: Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-Å cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19.

PubMed: 32970990
DOI: 10.1016/j.cell.2020.09.035

Experimental method

X-RAY DIFFRACTION (2.7 Å)