9e9o

SARS-CoV-2 SL5 crystal structure Cesium derivative

spinqualitylabelsall models 9e9o, resolution 3.51Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9e9o is a 1 chain structure with sequence from Severe acute respiratory syndrome coronavirus 2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.51Å Ligands: CS, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Stem-loop 5 (SL5) is a structural element that is conserved across coronavirus genomic RNAs. It spans the start codon from which the long ORF1 is translated in full-length viral RNA. Phylogenetic conservation indicates that it is comprised of four paired elements, but the specific 3D arrangement of these helices has remained unknown. Now, we have solved the crystal structure of SL5 from SARS-CoV-2 at 3.3 A resolution, finding that the RNA adopts a T-shaped four-way junction fold in which two coaxial stacks of two helices each pack orthogonally. This arrangement results in deep pockets at the helical junction, where cations bind. Except for limited interactions in this region, the structure is remarkable for the paucity of tertiary contacts. We confirmed the stability of this fold in solution by FRET and carried out single-particle cryogenic-sample electron microscopy (cryoEM). The resulting approximately 5 A resolution cryoEM map, and 3D variability analysis, suggest conformational flexibility at the junction. In vitro translation of structure-guided mutants demonstrated that SL5 inhibits protein synthesis. Thus, it is likely that SL5 recruits additional factors in vivo. This, and its characteristic clefts at the four-way junction, make SL5 an attractive target for the discovery of RNA-targeted antiviral small molecules. Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.,Jones CP, Ferre-D'Amare AR RNA. 2025 Jun 16;31(7):949-960. doi: 10.1261/rna.080413.125. PMID:40527531 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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