8ZHD
SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs
This is a non-PDB format compatible entry.
Summary for 8ZHD
| Entry DOI | 10.2210/pdb8zhd/pdb |
| EMDB information | 60099 |
| 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 More |
| Total number of polymer chains | 7 |
| Total formula weight | 539696.95 |
| Authors | |
| 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 Cited by 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: 39217172DOI: 10.1038/s41467-024-51770-3 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.41 Å) |
Structure validation
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