8JAM
Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Summary for 8JAM
| Entry DOI | 10.2210/pdb8jam/pdb |
| EMDB information | 36122 |
| Descriptor | Spike glycoprotein, H chain of W328-6H2, L chain of W328-6H2, ... (5 entities in total) |
| Functional Keywords | cryo-em, complex, omicron ba.1, antibody, homo sapiens, igg, rbd, local refinement, viral protein |
| Biological source | Severe acute respiratory syndrome-related coronavirus More |
| Total number of polymer chains | 3 |
| Total formula weight | 166544.09 |
| Authors | |
| Primary citation | Nan, X.,Li, Y.,Zhang, R.,Wang, R.,Lv, N.,Li, J.,Chen, Y.,Zhou, B.,Wang, Y.,Wang, Z.,Zhu, J.,Chen, J.,Li, J.,Chen, W.,Zhang, Q.,Shi, X.,Zhao, C.,Chen, C.,Liu, Z.,Zhao, Y.,Liu, D.,Wang, X.,Yan, L.T.,Li, T.,Zhang, L.,Yang, Y.R. Exploring distinct modes of inter-spike cross-linking for enhanced neutralization by SARS-CoV-2 antibodies. Nat Commun, 15:10578-10578, 2024 Cited by PubMed Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when binds fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, enriching our understanding of enhanced neutralization by SARS-CoV-2 antibodies. PubMed: 39632831DOI: 10.1038/s41467-024-54746-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.92 Å) |
Structure validation
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