9E9Q

SARS-CoV-2 SL5 crystal structure native

9E9Q の概要

• エントリーDOI: 10.2210/pdb9e9q/pdb
• EMDBエントリー: 47501
• 分子名称: RNA (101-MER), MAGNESIUM ION (3 entities in total)
• 機能のキーワード: utr, virus, coronavirus, 5' utr, untranslated region, translation, control, rna
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 2019-nCoV, COVID-19 virus)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 32653.78

構造登録者

Jones, C.P.,Ferre-D'Amare, A.R. (登録日: 2024-11-08, 公開日: 2025-07-09)

主引用文献

Jones, C.P.,Ferre-D'Amare, A.R.
Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.
Rna, 31:949-960, 2025

PubMed Abstract: 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 Å 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 ∼5 Å 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.

PubMed: 40527531
DOI: 10.1261/rna.080413.125

実験手法

X-RAY DIFFRACTION (3.33 Å)