3ND4

Watson-Crick 16-mer dsRNA

3ND4 の概要

• エントリーDOI: 10.2210/pdb3nd4/pdb
• 関連するPDBエントリー: 3ND3
• 分子名称: 5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3', MAGNESIUM ION, POTASSIUM ION, ... (5 entities in total)
• 機能のキーワード: double-stranded rna, rna, 16 base pair rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 5169.46

構造登録者

Mooers, B.H.,Singh, A. (登録日: 2010-06-07, 公開日: 2011-09-21, 最終更新日: 2024-02-21)

主引用文献

Mooers, B.H.,Singh, A.
The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.
Rna, 17:1870-1883, 2011

PubMed Abstract: Guide RNAs bind antiparallel to their target pre-mRNAs to form editing substrates in reaction cycles that insert or delete uridylates (Us) in most mitochondrial transcripts of trypanosomes. The 5' end of each guide RNA has an anchor sequence that binds to the pre-mRNA by base-pair complementarity. The template sequence in the middle of the guide RNA directs the editing reactions. The 3' ends of most guide RNAs have ∼15 contiguous Us that bind to the purine-rich unedited pre-mRNA upstream of the editing site. The resulting U-helix is rich in G·U wobble base pairs. To gain insights into the structure of the U-helix, we crystallized 8 bp of the U-helix in one editing substrate for the A6 mRNA of Trypanosoma brucei. The fragment provides three samples of the 5'-AGA-3'/5'-UUU-3' base-pair triple. The fusion of two identical U-helices head-to-head promoted crystallization. We obtained X-ray diffraction data with a resolution limit of 1.37 Å. The U-helix had low and high twist angles before and after each G·U wobble base pair; this variation was partly due to shearing of the wobble base pairs as revealed in comparisons with a crystal structure of a 16-nt RNA with all Watson-Crick base pairs. Both crystal structures had wider major grooves at the junction between the poly(U) and polypurine tracts. This junction mimics the junction between the template helix and the U-helix in RNA-editing substrates and may be a site of major groove invasion by RNA editing proteins.

PubMed: 21878548
DOI: 10.1261/rna.2880311

実験手法

X-RAY DIFFRACTION (1.524 Å)