8SFS
High Affinity nanobodies against GFP
Summary for 8SFS
| Entry DOI | 10.2210/pdb8sfs/pdb |
| Descriptor | Green fluorescent protein, LaG16, AMMONIUM ION, ... (8 entities in total) |
| Functional Keywords | nanobody, nanobodies, gfp, green fluorescent protein, high-affinity antibody variant, antibody variant, single-domain antibody, immune system |
| Biological source | Aequorea victoria More |
| Total number of polymer chains | 4 |
| Total formula weight | 92223.64 |
| Authors | Ketaren, N.E.,Rout, M.P.,Bonnano, J.B.,Almo, S.C. (deposition date: 2023-04-11, release date: 2024-05-22, Last modification date: 2025-06-04) |
| Primary citation | Ketaren, N.E.,Fridy, P.C.,Malashkevich, V.,Sanyal, T.,Brillantes, M.,Thompson, M.K.,Oren, D.A.,Bonanno, J.B.,Sali, A.,Almo, S.C.,Chait, B.T.,Rout, M.P. Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies. Structure, 33:677-690.e5, 2025 Cited by PubMed Abstract: Nanobodies are single domain antibody variants proving themselves to be compelling tools for research, disease diagnostics, and as therapeutics targeting a myriad of disease agents. However, despite this potential, their mechanisms of paratope presentation and structural stabilization have not been fully explored. Here, we show that unlike monoclonal antibodies, a nanobody repertoire maximizes sampling of an antigen surface by binding a single antigen in at least three different orientations, which are correlated with their paratope composition. Structure-guided reengineering of several nanobodies reveals that a single point mutation within the paratope or a highly conserved region of a nanobody's framework 3 (FR3) can markedly improve antigen affinity, nanobody stability, or both. Conversely, we show the negative impact on antigen affinity when "over-stabilizing" nanobodies. Collectively our results provide a universal strategy to tune a nanobody's affinity by modifying specific residues that can readily be applied to guide nanobody optimization and functionalization. PubMed: 39938509DOI: 10.1016/j.str.2025.01.019 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.37 Å) |
Structure validation
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