5GIN

Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates

5GIN の概要

• エントリーDOI: 10.2210/pdb5gin/pdb
• 関連するPDBエントリー: 5GIO 5GIP
• 分子名称: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit, 50S ribosomal protein L7Ae, Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase, ... (6 entities in total)
• 機能のキーワード: 2'-o-methylation, guide rna, rnp, transferase-rna complex, transferase/rna
• 由来する生物種: Sulfolobus solfataricus; 詳細
• 細胞内の位置: Cytoplasm : A0A0E3JZF7
• タンパク質・核酸の鎖数: 15
• 化学式量合計: 302376.13

構造登録者

Yang, Z.,Lin, J.,Ye, K. (登録日: 2016-06-24, 公開日: 2016-09-14, 最終更新日: 2023-11-08)

主引用文献

Yang, Z.,Lin, J.,Ye, K.
Box C/D guide RNAs recognize a maximum of 10 nt of substrates
Proc.Natl.Acad.Sci.USA, 113:10878-10883, 2016

PubMed Abstract: Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.

PubMed: 27625427
DOI: 10.1073/pnas.1604872113

実験手法

X-RAY DIFFRACTION (3.308 Å)