8TKK

Cryo-EM structure of RNA device 43 truncation mutant 3 (U100C), apo state

Summary for 8TKK

• Entry DOI: 10.2210/pdb8tkk/pdb
• Related: 8syk 8t50
• EMDB information: 41354
• Descriptor: RNA device 43 truncation mutant 3 (U100C), GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: rna device, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 35282.92

Authors

Stagno, J.R.,Deme, J.C.,Lee, Y.-T.,Wang, Y.-X.,Lea, S.M. (deposition date: 2023-07-25, release date: 2025-02-19, Last modification date: 2026-03-04)

Primary citation

Stagno, J.R.,Deme, J.C.,Dwivedi, V.,Lee, Y.T.,Lee, H.K.,Yu, P.,Chen, S.Y.,Fan, L.,Degenhardt, M.F.S.,Chari, R.,Young, H.A.,Lea, S.M.,Wang, Y.X.
Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Synthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here, we present multidisciplinary structural and biochemical data for a tetracycline (Tc)-responsive RNA device (D43) in both ligand-free and bound states, providing a structure-dynamical basis for signal transmission. Activation of self-cleavage is achieved via ligand-induced conformational and dynamical changes that stabilize the elongated bridging helix harboring the communication module, which drives proper coordination of the catalytic residues. We then show the utility of CRISPR-integrated D43 in EL4 lymphocytes to regulate programmed cell death protein 1 (PD-1), a key receptor of immune checkpoints. Treatment of these cells with Tc showed a dose-dependent reduction in PD-1 by immunostaining and a decrease in messenger RNA levels by quantitative PCR as compared with wild type. PD-1 expression was recoverable upon removal of Tc. These results provide mechanistic insight into RNA devices with potential for cancer immunotherapy or other applications.

PubMed: 40071935
DOI: 10.1093/nar/gkaf156

Experimental method

ELECTRON MICROSCOPY (3.37 Å)