8HWS

The complex structure of Omicron BA.4 RBD with BD604, S309, and S304

Summary for 8HWS

• Entry DOI: 10.2210/pdb8hws/pdb
• EMDB information: 35063
• Descriptor: Spike protein S2', BD-604 Fab Heavy chain, BD-604 Fab Light chain, ... (8 entities in total)
• Functional Keywords: antibody viral protein complex, immune system/viral protein, immune system-viral protein complex
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 7
• Total formula weight: 167169.33

Authors

He, Q.W.,Xu, Z.P.,Xie, Y.F. (deposition date: 2023-01-02, release date: 2023-12-06, Last modification date: 2024-10-23)

Primary citation

He, Q.,Wu, L.,Xu, Z.,Wang, X.,Xie, Y.,Chai, Y.,Zheng, A.,Zhou, J.,Qiao, S.,Huang, M.,Shang, G.,Zhao, X.,Feng, Y.,Qi, J.,Gao, G.F.,Wang, Q.
An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB.
Cell Rep Med, 4:100991-100991, 2023

PubMed Abstract: Emerging Omicron sub-variants are causing global concerns, and their immune evasion should be monitored continuously. We previously evaluated the escape of Omicron BA.1, BA.1.1, BA.2, and BA.3 from an atlas of 50 monoclonal antibodies (mAbs), covering seven epitope classes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain (RBD). Here, we update the atlas of totally 77 mAbs against emerging sub-variants including BQ.1.1 and XBB and find that BA.4/5, BQ.1.1, and XBB display further evasion. Besides, investigation into the correlation of binding and neutralization of mAbs reveals the important role of antigenic conformation in mAb functioning. Moreover, the complex structures of BA.2 RBD/BD-604/S304 and BA.4/5 RBD/BD-604/S304/S309 further elucidate the molecular mechanism of antibody evasion by these sub-variants. By focusing on the identified broadly potent mAbs, we find a general hotspot epitope on the RBD, which could guide the design of vaccines and calls for new broad-spectrum countermeasures against COVID-19.

PubMed: 37019110
DOI: 10.1016/j.xcrm.2023.100991

Experimental method

ELECTRON MICROSCOPY (2.36 Å)