7E9I
Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe
Summary for 7E9I
| Entry DOI | 10.2210/pdb7e9i/pdb |
| Descriptor | 33-mer RNA, 2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | preq1 riboswitch, cognate ligand-derived photoaffinity probe, rna |
| Biological source | Caldanaerobacter subterraneus subsp. tengcongensis |
| Total number of polymer chains | 1 |
| Total formula weight | 10994.81 |
| Authors | Numata, T.,Schneekloth, J.S. (deposition date: 2021-03-04, release date: 2021-11-17, Last modification date: 2023-11-29) |
| Primary citation | Balaratnam, S.,Rhodes, C.,Bume, D.D.,Connelly, C.,Lai, C.C.,Kelley, J.A.,Yazdani, K.,Homan, P.J.,Incarnato, D.,Numata, T.,Schneekloth Jr., J.S. A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites. Nat Commun, 12:5856-5856, 2021 Cited by PubMed Abstract: The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ riboswitch system, assessing sixteen diverse PreQ-derived probes for their ability to selectively modify the class-I PreQ riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ, which is similar in structure to guanine, interacts with human RNAs. PubMed: 34615874DOI: 10.1038/s41467-021-25973-x PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
Download full validation report
