8EYV

Structure of Beetroot dimer bound to DFHO

8EYV の概要

• エントリーDOI: 10.2210/pdb8eyv/pdb
• 分子名称: RNA (45-MER), POTASSIUM ION, (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one, ... (4 entities in total)
• 機能のキーワード: rna, aptamer, fluorescence, turn-on, fluorogenic, fluorophore, g-quartet, g-quadruplex
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 32804.94

構造登録者

Passalacqua, L.F.M.,Ferre-D'Amare, A.R. (登録日: 2022-10-28, 公開日: 2023-05-31, 最終更新日: 2023-10-25)

主引用文献

Passalacqua, L.F.M.,Starich, M.R.,Link, K.A.,Wu, J.,Knutson, J.R.,Tjandra, N.,Jaffrey, S.R.,Ferre-D'Amare, A.R.
Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Nat Commun, 14:2969-2969, 2023

PubMed Abstract: Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

PubMed: 37221204
DOI: 10.1038/s41467-023-38683-3

実験手法

X-RAY DIFFRACTION (2.55 Å)