9HRF

Crystal structure of the Class V (UU) GTP aptamer variant in complex with GTP

9HRF の概要

• エントリーDOI: 10.2210/pdb9hrf/pdb
• 分子名称: Class V (UU) GTP aptamer, GUANOSINE-5'-TRIPHOSPHATE, POTASSIUM ION, ... (6 entities in total)
• 機能のキーワード: rna-aptamer gtp g-quadruplex potassium ion, rna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23362.61

構造登録者

Stafflinger, H.,Woehnert, J.,Schindelin, H. (登録日: 2024-12-18, 公開日: 2026-01-14)

主引用文献

Stafflinger, H.,Neissner, K.,Bartsch, S.,Pichler, A.K.,Bartosik, K.,Dhamotharan, K.,Abele, R.,Duchardt-Ferner, E.,Micura, R.,Schindelin, H.,Wohnert, J.
Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: RNA aptamers obtained from in vitro selection experiments provide unique insights into the structural properties and ligand recognition capabilities of RNA in general. In order to investigate the relationships between RNA sequence information content and structural complexity with ligand affinity and specificity, the Szostak group previously identified eleven different families of GTP-binding aptamers varying widely in their sequence conservation patterns as well as in their secondary structure complexity and topology. The class V GTP aptamer has a particularly high affinity for GTP. Here, we report the high-resolution X-ray crystal structure of this aptamer-GTP complex. Remarkably, GTP is found to be integrated into one layer of a two-layered G-quadruplex, thereby rationalizing the high ligand affinity and the observed specificity. The G-quadruplex is extended on one side by a noncanonical tetrad layer containing three non-G nucleotides and on the other side by a Watson-Crick base pair stacking on top of an unpaired adenine. Interestingly, the G-nucleotides forming the G-quadruplex originate from two asymmetric bulges separated by an 8 base pair A-form helix, resulting in a complex and previously unobserved G-quadruplex topology.

PubMed: 41422825
DOI: 10.1093/nar/gkaf1315

実験手法

X-RAY DIFFRACTION (1.6 Å)