8HR2

Ternary Crystal Complex Structure of RBD with NB1B5 and NB1C6

Summary for 8HR2

• Entry DOI: 10.2210/pdb8hr2/pdb
• Descriptor: Spike protein S1, NB1C6, NB1B5, ... (4 entities in total)
• Functional Keywords: sars-cov-2, rbd, nanobody, complex., structural protein, structural protein-immune system complex, structural protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 3
• Total formula weight: 52232.84

Authors

Sun, Z. (deposition date: 2022-12-14, release date: 2023-08-16, Last modification date: 2024-10-30)

Primary citation

Sun, Z.,Wang, L.,Li, L.,Sun, Y.,Zhang, D.,Zhou, S.,Li, Y.,Li, X.,Qiao, H.,Cui, Q.,Lan, Z.,Meng, X.,Xu, J.,Geng, Y.,Dai, Y.
Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes.
J.Struct.Biol., 215:107996-107996, 2023

PubMed Abstract: The evolving SARS-CoV-2 Omicron strain has repeatedly caused widespread disease epidemics, and effective antibody drugs continue to be in short supply. Here, we identified a batch of nanobodies with high affinity for receptor binding domain (RBD) of SARS-CoV-2 spike protein, separated them into three classes using high performance liquid chromatography (HPLC), and then resolved the crystal structure of the ternary complexes of two non-competing nanobodies (NB1C6 and NB1B5) with RBD using X-ray crystallography. The structures showed that NB1B5 and NB1C6 bind to the left and right flank of the RBD, respectively, and that the binding epitopes are highly conserved cryptic sites in all SARS-CoV-2 mutant strains, as well as that NB1B5 can effectively block the ACE2. These two nanobodies were covalently linked into multivalent and bi-paratopic formats, and have a high affinity and neutralization potency for omicron, potentially inhibiting viral escape. The binding sites of these two nanobodies are relatively conserved, which help guide the structural design of antibodies targeting future variants of SARS-CoV-2 to combat COVID-19 epidemics and pandemics.

PubMed: 37419228
DOI: 10.1016/j.jsb.2023.107996

Experimental method

X-RAY DIFFRACTION (1.94 Å)