9L6Z

Crystal structure of the L7Ae derivative protein LS12 in RNA-free state

Summary for 9L6Z

• Entry DOI: 10.2210/pdb9l6z/pdb
• Descriptor: Large ribosomal subunit protein eL8, SODIUM ION (3 entities in total)
• Functional Keywords: protein-rna complex, rna binding protein
• Biological source: Archaeoglobus fulgidus DSM 4304
• Total number of polymer chains: 2
• Total formula weight: 26315.18

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

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: 40119732
DOI: 10.1093/nar/gkaf212

Experimental method

X-RAY DIFFRACTION (1.8 Å)