8DW9
Crystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)
Summary for 8DW9
| Entry DOI | 10.2210/pdb8dw9/pdb |
| Descriptor | Spike protein S1, D29 Heavy chain, D29 Fab light chain (3 entities in total) |
| Functional Keywords | covid-19, sarbecovirus, wiv1 rbd, viral protein, spike glycoprotein, receptor binding protein, neutralizing antibody, potent, 10-40, fab, 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 | 6 |
| Total formula weight | 135949.96 |
| Authors | Reddem, E.R.,Shapiro, L. (deposition date: 2022-08-01, release date: 2022-12-07, Last modification date: 2024-11-20) |
| Primary citation | Luo, M.,Zhou, B.,Reddem, E.R.,Tang, B.,Chen, B.,Zhou, R.,Liu, H.,Liu, L.,Katsamba, P.S.,Au, K.K.,Man, H.O.,To, K.K.,Yuen, K.Y.,Shapiro, L.,Dang, S.,Ho, D.D.,Chen, Z. Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Emerg Microbes Infect, 12:2146538-2146538, 2023 Cited by PubMed Abstract: Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis. PubMed: 36354024DOI: 10.1080/22221751.2022.2146538 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (4 Å) |
Structure validation
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