8Z2E
Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
Summary for 8Z2E
| Entry DOI | 10.2210/pdb8z2e/pdb |
| Descriptor | Tnb04-1, Spike protein S1, 1F11-H, ... (6 entities in total) |
| Functional Keywords | sars-cov-2, neutralizing nanobody, antibody, conserved epitope, viral protein/immune system, viral protein-immune system complex |
| Biological source | Vicugna pacos More |
| Total number of polymer chains | 4 |
| Total formula weight | 83810.55 |
| Authors | Wang, X.Q.,Zhang, L.Q.,Chen, J.,Dong, H.D. (deposition date: 2024-04-12, release date: 2025-04-23, Last modification date: 2025-11-05) |
| Primary citation | Dong, H.,Zhou, R.,Chen, J.,Wei, J.,Wei, Z.,Yang, Z.,Zhu, K.,Yang, Y.,Yang, Q.,Liu, N.,Chen, Y.,Wu, Y.,Liang, Y.,Zeng, Y.,Guo, Q.,Li, M.,Shan, S.,Wang, H.,Niu, M.,Yunfei Zeng, I.,Shi, X.,Zhang, Q.,Wang, X.,Chen, Z.,Zhang, L. Super broad and protective nanobodies against Sarbecoviruses including SARS-CoV-1 and the divergent SARS-CoV-2 subvariant KP.3.1.1. Plos Pathog., 20:e1012625-e1012625, 2024 Cited by PubMed Abstract: The ongoing evolution and immune escape of SARS-CoV-2, alongside the potential threat of SARS-CoV-1 and other sarbecoviruses, underscore the urgent need for effective strategies against their infection and transmission. This study highlights the discovery of nanobodies from immunized alpacas, which demonstrate exceptionally broad and potent neutralizing capabilities against the recently emerged and more divergent SARS-CoV-2 Omicron subvariants including JD.1.1, JN.1, KP.3, KP.3.1.1, as well as SARS-CoV-1 and coronaviruses from bats and pangolins utilizing receptor ACE2. Among these, Tnb04-1 emerges as the most broad and potent, binding to a conserved hydrophobic pocket in the spike's receptor-binding domain, distinct from the ACE2 binding site. This interaction disrupts the formation of a proteinase K-resistant core, crucial for viral-cell fusion. Notably, intranasal administration of Tnb04-1 in Syrian hamsters effectively prevented respiratory infection and transmission of the authentic Omicron XBB.1.5 subvariant. Thus, Thb04-1 holds promise in combating respiratory acquisition and transmission of diverse sarbecoviruses. PubMed: 39527594DOI: 10.1371/journal.ppat.1012625 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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