9KZE
The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-183
Summary for 9KZE
| Entry DOI | 10.2210/pdb9kze/pdb |
| EMDB information | 62661 |
| Descriptor | XGi-183 heavy chain, XGi-183 light chain, Spike glycoprotein, ... (4 entities in total) |
| Functional Keywords | spike-antibody complex, viral protein/immune system, viral protein-immune system complex |
| Biological source | Homo sapiens More |
| Total number of polymer chains | 3 |
| Total formula weight | 215695.52 |
| Authors | |
| Primary citation | Xie, M.,Qiu, Y.,Zhao, X.,Shi, J.,Liu, Y.,Zhang, Q.,He, J.,Li, J.,Liu, L.,Sun, S.,Zhu, Y.,Mao, Q.,Long, Y.,Oliveira, T.Y.,Wang, Z.,Zhou, Y.,Yan, Y.,Xia, A.,Zai, W.,Mayer, C.T.,Xie, Y.,Jiang, S.,Lu, L.,Xia, R.,Wu, F.,Sun, L.,Wang, P.,Chu, H.,Wang, Q. Orphan broadly RBD-binding antibodies annotate three remaining conserved RBD epitopes along SARS-CoV-2 evolution. Nat Commun, 16:10566-10566, 2025 Cited by PubMed Abstract: The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein continues to evolve, facilitating antibody evasion. It remains unclear whether any conserved RBD epitopes persist across SARS-CoV-2 variants and whether vaccination and/or breakthrough infection (BTI) can elicit antibodies capable of targeting these conserved regions to counter future variants. Here, using a heterogeneous double-bait single B-cell sorting strategy, we identify a subset of antibodies with broad-spectrum RBD binding, including recognition of SARS-CoV-1 and emerging variants such as EG.5.1, BA.2.86, JN.1, and KP.2/3. These broadly binding antibodies (bbAbs) exhibit elevated levels of somatic hypermutation but are infrequently derived from clonally expanded B lymphocytes. Passive transfer of representative bbAbs reduces viral infection in a male hamster model. Structural analyses reveals that these bbAbs primarily target three distinct, highly conserved RBD epitopes, suggesting potential regions of future mutational pressure and highlighting the presence of conserved and immunogenic RBD conformations that may serve as a foundation for the development of broadly protective vaccines. PubMed: 41298374DOI: 10.1038/s41467-025-65596-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.4 Å) |
Structure validation
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