8ZHP

Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs

Summary for 8ZHP

• Entry DOI: 10.2210/pdb8zhp/pdb
• Related: 8ZHD 8ZHE 8ZHF 8ZHG 8ZHH 8ZHI 8ZHJ 8ZHK 8ZHL 8ZHM 8ZHN 8ZHO
• EMDB information: 60111
• Descriptor: Spike glycoprotein, Heavy chain of R1-32 Fab, Light chain of R1-32 Fab, ... (6 entities in total)
• Functional Keywords: spike protein, rbd, antibody, fab, viral protein, viral protein-immune system complex, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 10
• Total formula weight: 345191.83

Authors

Yan, Q.,Gao, X.,Liu, B.,Hou, R.,He, P.,Li, Z.,Chen, Q.,Wang, J.,He, J.,Chen, L.,Zhao, J.,Xiong, X. (deposition date: 2024-05-11, release date: 2024-08-21, Last modification date: 2024-10-23)

Primary citation

Yan, Q.,Gao, X.,Liu, B.,Hou, R.,He, P.,Ma, Y.,Zhang, Y.,Zhang, Y.,Li, Z.,Chen, Q.,Wang, J.,Huang, X.,Liang, H.,Zheng, H.,Yao, Y.,Chen, X.,Niu, X.,He, J.,Chen, L.,Zhao, J.,Xiong, X.
Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants.
Nat Commun, 15:7585-7585, 2024

PubMed Abstract: Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.

PubMed: 39217172
DOI: 10.1038/s41467-024-51770-3

Experimental method

ELECTRON MICROSCOPY (3.66 Å)