7MF1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1

Summary for 7MF1

• Entry DOI: 10.2210/pdb7mf1/pdb
• Descriptor: Spike protein S1, 47D1 Fab heavy chain, 47D1 Fab light chain, ... (6 entities in total)
• Functional Keywords: covid-19, immune system-viral protein complex, immune system/viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 3
• Total formula weight: 71136.23

Authors

Yuan, M.,Zhu, X.,Wilson, I.A. (deposition date: 2021-04-08, release date: 2021-05-12, Last modification date: 2024-11-06)

Primary citation

Zhou, X.,Ma, F.,Xie, J.,Yuan, M.,Li, Y.,Shaabani, N.,Zhao, F.,Huang, D.,Wu, N.C.,Lee, C.D.,Liu, H.,Li, J.,Chen, Z.,Hong, Y.,Liu, W.H.,Xiao, N.,Burton, D.R.,Tu, H.,Li, H.,Chen, X.,Teijaro, J.R.,Wilson, I.A.,Xiao, C.,Huang, Z.
Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2.
Cell Rep, 35:109109-109109, 2021

PubMed Abstract: It is unclear whether individuals with enormous diversity in B cell receptor repertoires are consistently able to mount effective antibody responses against SARS-CoV-2. We analyzed antibody responses in a cohort of 55 convalescent patients and isolated 54 potent neutralizing monoclonal antibodies (mAbs). While most of the mAbs target the angiotensin-converting enzyme 2 (ACE2) binding surface on the receptor binding domain (RBD) of SARS-CoV-2 spike protein, mAb 47D1 binds only to one side of the receptor binding surface on the RBD. Neutralization by 47D1 is achieved independent of interfering RBD-ACE2 binding. A crystal structure of the mAb-RBD complex shows that the IF motif at the tip of 47D1 CDR H2 interacts with a hydrophobic pocket in the RBD. Diverse immunoglobulin gene usage and convergent epitope targeting characterize neutralizing antibody responses to SARS-CoV-2, suggesting that vaccines that effectively present the receptor binding site on the RBD will likely elicit neutralizing antibody responses in a large fraction of the population.

PubMed: 33932326
DOI: 10.1016/j.celrep.2021.109109

Experimental method

X-RAY DIFFRACTION (2.092 Å)