9L6Y
Crystal structure of the L7Ae derivative protein LS12 in complex with its co-evolved target CS2 RNA
Summary for 9L6Y
| Entry DOI | 10.2210/pdb9l6y/pdb |
| Descriptor | Large ribosomal subunit protein eL8, CS2 RNA, CALCIUM ION (3 entities in total) |
| Functional Keywords | protein-rna complex, rna binding protein |
| Biological source | Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) More |
| Total number of polymer chains | 4 |
| Total formula weight | 47711.50 |
| Authors | Teramoto, T.,Nakashima, M.,Fukunaga, K.,Yokobayashi, Y.,Kakuta, Y. (deposition date: 2024-12-25, release date: 2025-04-02) |
| Primary citation | Fukunaga, K.,Teramoto, T.,Nakashima, M.,Ohtani, T.,Katsuki, R.,Matsuura, T.,Yokobayashi, Y.,Kakuta, Y. Structural insights into lab-coevolved RNA-RBP pairs and applications of synthetic riboswitches in cell-free system. Nucleic Acids Res., 53:-, 2025 Cited by PubMed Abstract: CS1-LS4 and CS2-LS12 are ultra-high affinity and orthogonal RNA-protein pairs that were identified by PD-SELEX (Phage Display coupled with Systematic Evolution of Ligands by EXponential enrichment). To investigate the molecular basis of the lab-coevolved RNA-RBP pairs, we determined the structures of the CS1-LS4 and CS2-LS12 complexes and the LS12 homodimer in an RNA-free state by X-ray crystallography. The structural analyses revealed that the lab-coevolved RNA-RBPs have acquired unique molecular recognition mechanisms, whereas the overall structures of the RNP complexes were similar to the typical kink-turn RNA-L7Ae complex. The orthogonal RNA-RBP pairs were applied to construct high-performance cell-free riboswitches that regulate translation in response to LS4 or LS12. In addition, by using the orthogonal protein-responsive switches, we generated an AND logic gate that outputs staphylococcal γ-hemolysin in cell-free system and carried out hemolysis assay and calcein leakage assay using rabbit red blood cells and artificial cells, respectively. PubMed: 40119732DOI: 10.1093/nar/gkaf212 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.12 Å) |
Structure validation
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