4PDB

CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER

4PDB の概要

• エントリーDOI: 10.2210/pdb4pdb/pdb
• 関連するPDBエントリー: 2LUN
• 分子名称: 30S ribosomal protein S8, SELEX RNA aptamer (3 entities in total)
• 機能のキーワード: protein-rna complex selex base triple translation, ribosomal protein-rna complex, ribosomal protein/rna
• 由来する生物種: Bacillus anthracis; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 29576.45

構造登録者

Davlieva, M.,Shamoo, Y.,Nikonowicz, E.P. (登録日: 2014-04-17, 公開日: 2014-09-03, 最終更新日: 2023-12-27)

主引用文献

Davlieva, M.,Donarski, J.,Wang, J.,Shamoo, Y.,Nikonowicz, E.P.
Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.
Nucleic Acids Res., 42:10795-10808, 2014

PubMed Abstract: Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.

PubMed: 25140011
DOI: 10.1093/nar/gku743

実験手法

X-RAY DIFFRACTION (2.6 Å)