8ZHE

SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs

Summary for 8ZHE

• Entry DOI: 10.2210/pdb8zhe/pdb
• Related: 8ZHD
• EMDB information: 60100
• Descriptor: Spike glycoprotein,Fibritin,Expression Tag, Heavy chain of R1-26 Fab, Light chain of R1-26 Fab, ... (5 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 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 9
• Total formula weight: 591163.48

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: 2024-05-10, 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 (3.16 Å)