7KLW
Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain
Summary for 7KLW
| Entry DOI | 10.2210/pdb7klw/pdb |
| Related | 7KGJ 7KGK 7KGL |
| Descriptor | Spike protein S1, SB45, Synthetic Nanobody, SB68, Synthetic nanobody, ... (4 entities in total) |
| Functional Keywords | sars-cov-2, spike protein, receptor binding domain, rbd, antibody, nanobody, sybody, complex, neutralization, viral protein, epitope |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) More |
| Total number of polymer chains | 3 |
| Total formula weight | 48982.46 |
| Authors | Jiang, J.,Ahmad, J.,Natarajan, K.,Boyd, L.F.,Margulies, D.H. (deposition date: 2020-11-01, release date: 2021-02-03, Last modification date: 2024-11-20) |
| Primary citation | Ahmad, J.,Jiang, J.,Boyd, L.F.,Zeher, A.,Huang, R.,Xia, D.,Natarajan, K.,Margulies, D.H. Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem., 297:101202-101202, 2021 Cited by PubMed Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures. PubMed: 34537245DOI: 10.1016/j.jbc.2021.101202 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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