5TDK

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

Summary for 5TDK

• Entry DOI: 10.2210/pdb5tdk/pdb
• Related: 4MS9 4MSB 4MSR 5TDJ
• Descriptor: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'), STRONTIUM ION (3 entities in total)
• Functional Keywords: 2'-5'-linkage, rna, plant protein
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 6852.06

Authors

Luo, Z.,Sheng, J. (deposition date: 2016-09-19, release date: 2017-01-11, Last modification date: 2023-10-04)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.43 Å)