8CQ1

Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA

8CQ1 の概要

• エントリーDOI: 10.2210/pdb8cq1/pdb
• NMR情報: BMRB: 50347,50760
• 分子名称: 5_SL4 (1 entity in total)
• 機能のキーワード: sars-cov2, stem-loop, rna
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 14074.32

構造登録者

Duchardt-Ferner, E.,Voegele, J. (登録日: 2023-03-03, 公開日: 2023-09-20, 最終更新日: 2023-11-22)

主引用文献

Vogele, J.,Hymon, D.,Martins, J.,Ferner, J.,Jonker, H.R.A.,Hargrove, A.E.,Weigand, J.E.,Wacker, A.,Schwalbe, H.,Wohnert, J.,Duchardt-Ferner, E.
High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.
Nucleic Acids Res., 51:11318-11331, 2023

PubMed Abstract: We present the high-resolution structure of stem-loop 4 of the 5'-untranslated region (5_SL4) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) genome solved by solution state nuclear magnetic resonance spectroscopy. 5_SL4 adopts an extended rod-like structure with a single flexible looped-out nucleotide and two mixed tandem mismatches, each composed of a G•U wobble base pair and a pyrimidine•pyrimidine mismatch, which are incorporated into the stem-loop structure. Both the tandem mismatches and the looped-out residue destabilize the stem-loop structure locally. Their distribution along the 5_SL4 stem-loop suggests a role of these non-canonical elements in retaining functionally important structural plasticity in particular with regard to the accessibility of the start codon of an upstream open reading frame located in the RNA's apical loop. The apical loop-although mostly flexible-harbors residual structural features suggesting an additional role in molecular recognition processes. 5_SL4 is highly conserved among the different variants of SARS-CoV-2 and can be targeted by small molecule ligands, which it binds with intermediate affinity in the vicinity of the non-canonical elements within the stem-loop structure.

PubMed: 37791874
DOI: 10.1093/nar/gkad762

実験手法

SOLUTION NMR