8XS1
Crystal structure of Fab fragment of anti-osteocalcin antibody KTM219 complexed with C-terminal peptide antigen
Summary for 8XS1
| Entry DOI | 10.2210/pdb8xs1/pdb |
| Related | 5X5X |
| Descriptor | Heavy chain fragment (Fd) chain of anti-osteocalcin antibody KTM219, Light chain of anti-osteocalcin antibody KTM219, Osteocalcin, ... (4 entities in total) |
| Functional Keywords | antibody, immunoglobulin fold, osteocalcin, quenchbody (q-body), open sandwich immunoassay, immune system |
| Biological source | Mus musculus More |
| Total number of polymer chains | 3 |
| Total formula weight | 52358.87 |
| Authors | Komatsu, M.,Dong, J.,Ueda, H.,Arai, R. (deposition date: 2024-01-08, release date: 2025-01-15, Last modification date: 2025-02-05) |
| Primary citation | Yazaki, S.,Komatsu, M.,Dong, J.,Ueda, H.,Arai, R. Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219. Int J Mol Sci, 26:-, 2025 Cited by PubMed Abstract: Osteocalcin is a useful biomarker for bone formation and bone-related diseases. KTM219 is an anti-osteocalcin C-terminal peptide antibody. The single-chain variable region (scFv) and antigen-binding fragment (Fab) of KTM219 are applicable to the Quenchbody (Q-body) immunoassay. Q-body is a new type of fluorescent immunosensor, which is scFv or Fab labeled with a fluorescent dye. When Q-body binds to its antigen, the fluorescence intensity increases. The highly sensitive detection of antigens by changes in fluorescence intensity is performed in a single step by mixing the sample and reagent. In this study, to reveal the recognition mechanism of the KTM219 antibody and to discuss the structural basis for Q-body, we solved the crystal structures of Fab of the anti-osteocalcin antibody KTM219 and its complex with the antigen osteocalcin C-terminal peptide (BGP-C7). Also, we solved the structure of a KTM219 Fab crystal grown in the presence of a fluorescent dye, carboxytetramethylrhodamine (TAMRA); however, tightly bound TAMRA was not found in the electron density map. We predicted the binding sites of TAMRA in the antigen-binding pocket by docking simulations. These results support the proposed Q-body mechanism. The crystal structures of KTM219 Fab would be useful for further development and improvement of Q-body fluorescent immunosensors. PubMed: 39859361DOI: 10.3390/ijms26020648 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
Download full validation report
