9CFN

Crystal structure of an exoribonuclease-resistant RNA from a Tombusvirus-like associated RNA

Summary for 9CFN

• Entry DOI: 10.2210/pdb9cfn/pdb
• Descriptor: RNA (59-MER), IRIDIUM HEXAMMINE ION, MAGNESIUM ION (3 entities in total)
• Functional Keywords: xrrna, pseudoknot, rna
• Biological source: Beet western yellows ST9 associated virus
• Total number of polymer chains: 2
• Total formula weight: 45138.92

Authors

Gezelle, J.,Wimberly, B.,Gong, Z.,Steckelberg, A.L. (deposition date: 2024-06-27, release date: 2025-07-16, Last modification date: 2025-09-10)

Primary citation

Gezelle, J.G.,Korn, S.M.,McDonald, J.T.,Gong, Z.,Erickson, A.,Huang, C.H.,Yang, F.,Cronin, M.,Kuo, Y.W.,Wimberly, B.T.,Steckelberg, A.L.
A conserved viral RNA fold enables nuclease resistance across kingdoms of life.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif-a protective ring encircling the RNA's 5' end-despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

PubMed: 40884403
DOI: 10.1093/nar/gkaf840

Experimental method

X-RAY DIFFRACTION (2.9 Å)