5TDJ

RNA decamer duplex with four 2'-5'-linkages

5TDJ の概要

• エントリーDOI: 10.2210/pdb5tdj/pdb
• 関連するPDBエントリー: 4MS9 4MSB 4MSR 5TDK
• 分子名称: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'), STRONTIUM ION (3 entities in total)
• 機能のキーワード: 2'-5'-linkage, rna, plant protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6501.58

構造登録者

Luo, Z.,Sheng, J. (登録日: 2016-09-19, 公開日: 2017-01-11, 最終更新日: 2023-10-04)

主引用文献

Shen, F.,Luo, Z.,Liu, H.,Wang, R.,Zhang, S.,Gan, J.,Sheng, J.
Structural insights into RNA duplexes with multiple 2 -5 -linkages.
Nucleic Acids Res., 45:3537-3546, 2017

PubMed Abstract: 2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.

PubMed: 28034958
DOI: 10.1093/nar/gkw1307

実験手法

X-RAY DIFFRACTION (1.5 Å)