8ZPU
Crystal structure of the anti-phosphorylated peptide C7 scFv antibody with peptide bound
Summary for 8ZPU
| Entry DOI | 10.2210/pdb8zpu/pdb |
| Descriptor | scFv, PHE-PRO-GLN-PHE-SEP-TYR-SER, SULFATE ION, ... (5 entities in total) |
| Functional Keywords | phosphorylated peptide, antibody, immune system |
| Biological source | Oryctolagus cuniculus More |
| Total number of polymer chains | 4 |
| Total formula weight | 57213.14 |
| Authors | Caaveiro, J.M.M.,Kawade, R.,Tsumoto, K. (deposition date: 2024-05-31, release date: 2024-12-11, Last modification date: 2024-12-25) |
| Primary citation | Kasahara, K.,Kawade, R.,Nakakido, M.,Matsunaga, R.,Akiba, H.,Entzminger, K.C.,Maruyama, T.,Okumura, S.C.J.,Caaveiro, J.M.M.,Kuroda, D.,Tsumoto, K. Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies. J.Biol.Chem., 300:107989-107989, 2024 Cited by PubMed Abstract: Protein phosphorylation is a crucial process in various cellular functions, and its irregularities have been implicated in several diseases, including cancer. Antibodies are commonly employed to detect protein phosphorylation in research. However, unlike the extensive studies on recognition mechanisms of the phosphate group by proteins such as kinases and phosphatases, only a few studies have explored antibody mechanisms. In this study, we produced and characterized two rabbit monoclonal antibodies that recognize a monophosphorylated Akt peptide. Through crystallography, thermodynamic mutational analyses, and molecular dynamics simulations, we investigated the unique recognition mechanism that enables higher binding affinity and selectivity of the antibodies compared to other generic proteins with lower binding affinity to phosphorylated epitopes. Our results demonstrate that molecular dynamics simulations provide novel insights into the dynamic aspects of molecular recognition of posttranslational modifications by proteins beyond static crystal structures, highlighting how specific atomic level interactions drive the exceptional affinity and selectivity of antibodies. PubMed: 39542251DOI: 10.1016/j.jbc.2024.107989 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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