4KZD

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

4KZD の概要

• エントリーDOI: 10.2210/pdb4kzd/pdb
• 関連するPDBエントリー: 3IVK 4KZE
• 関連するBIRD辞書のPRD_ID: PRD_900003
• 分子名称: BL3-6 Fab antibody, heavy chain, BL3-6 Fab antibody, light chain, RNA (84-MER), ... (8 entities in total)
• 機能のキーワード: g-quadruplex, fluorescence, fluorophore binding, in vitro, immune system-rna complex, immune system/rna
• 由来する生物種: Mus musculus (mouse); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 76086.59

構造登録者

Huang, H.,Suslov, N.B.,Li, N.,Koldobskaya, Y.,Rice, P.A.,Piccirilli, J.A. (登録日: 2013-05-29, 公開日: 2014-06-18, 最終更新日: 2024-11-20)

主引用文献

Huang, H.,Suslov, N.B.,Li, N.S.,Shelke, S.A.,Evans, M.E.,Koldobskaya, Y.,Rice, P.A.,Piccirilli, J.A.
A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol., 10:686-691, 2014

PubMed Abstract: Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.

PubMed: 24952597
DOI: 10.1038/nchembio.1561

実験手法

X-RAY DIFFRACTION (2.186 Å)