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Structure paper

TitleStructural investigation of an RNA device that regulates PD-1 expression in mammalian cells.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 5, Year 2025
Publish dateFeb 27, 2025
AuthorsJason R Stagno / Justin C Deme / Vibha Dwivedi / Yun-Tzai Lee / Hyun Kyung Lee / Ping Yu / Szu-Yun Chen / Lixin Fan / Maximilia F S Degenhardt / Raj Chari / Howard A Young / Susan M Lea / Yun-Xing Wang
PubMed AbstractSynthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here, we present multidisciplinary structural and ...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.
External linksNucleic Acids Res / PubMed:40071935 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.98 - 3.37 Å
Structure data

41059

8t5o

EMDB-41059, PDB-8t5o:
Cryo-EM structure of RNA device 43, holo state
Method: EM (single particle) / Resolution: 2.98 Å

41353

8tkj

EMDB-41353, PDB-8tkj:
Cryo-EM structure of RNA device 43, apo state
Method: EM (single particle) / Resolution: 3.2 Å

41354

8tkk

EMDB-41354, PDB-8tkk:
Cryo-EM structure of RNA device 43 truncation mutant 3 (U100C), apo state
Method: EM (single particle) / Resolution: 3.37 Å

PDB-8syk:
Crystal structure of RNA device 43 truncation mutant 3 (U100C), holo state
Method: X-RAY DIFFRACTION / Resolution: 3.06 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-TAC:
TETRACYCLINE / medication, antibiotic*YM

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • synthetic construct (others)
KeywordsRNA / RNA device / aptazyme / tetracycline riboswitch / ribozyme

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