6DB8

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

6DB8 の概要

• エントリーDOI: 10.2210/pdb6db8/pdb
• 分子名称: Fab-Heavy chain, RNA (60-MER), Fab-Light chain, ... (5 entities in total)
• 機能のキーワード: fluorescent aptamer, fab, dir, rna, rna-immune system complex, rna/immune system
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 67525.16

構造登録者

Shao, Y.,Shelke, S.A.,Laski, A.,Piccirilli, J.A. (登録日: 2018-05-02, 公開日: 2018-11-14, 最終更新日: 2024-11-06)

主引用文献

Shelke, S.A.,Shao, Y.,Laski, A.,Koirala, D.,Weissman, B.P.,Fuller, J.R.,Tan, X.,Constantin, T.P.,Waggoner, A.S.,Bruchez, M.P.,Armitage, B.A.,Piccirilli, J.A.
Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.
Nat Commun, 9:4542-4542, 2018

PubMed Abstract: The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.

PubMed: 30382099
DOI: 10.1038/s41467-018-06942-3

実験手法

X-RAY DIFFRACTION (1.86541345549 Å)