8UTG

An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome

Summary for 8UTG

• Entry DOI: 10.2210/pdb8utg/pdb
• Descriptor: RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3'), AMMONIUM ION, POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: rna quadruplex, g-quadruplex, g-tetrad, west nile virus, orthoflavivirus, rna
• Biological source: West Nile virus strain NY-99
• Total number of polymer chains: 2
• Total formula weight: 13832.51

Authors

Terrell, J.R.,Le, T.T.,Wilson, W.D.,Siemer, J.L. (deposition date: 2023-10-31, release date: 2024-06-19, Last modification date: 2024-07-17)

Primary citation

Terrell, J.R.,Le, T.T.,Paul, A.,Brinton, M.A.,Wilson, W.D.,Poon, G.M.K.,Germann, M.W.,Siemer, J.L.
Structure of an RNA G-quadruplex from the West Nile virus genome.
Nat Commun, 15:5428-5428, 2024

PubMed Abstract: Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.

PubMed: 38926367
DOI: 10.1038/s41467-024-49761-5

Experimental method

X-RAY DIFFRACTION (1.97 Å)