7kvu | pdb_00007kvu

Crystal structure of Squash RNA aptamer in complex with DFHBI-1T

spinqualitylabelsall models 7kvu, resolution 2.68Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7kvu is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.68Å Ligands: 2ZY, GTP, K, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-A resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.,Truong L, Kooshapur H, Dey SK, Li X, Tjandra N, Jaffrey SR, Ferre-D'Amare AR Nat Chem Biol. 2021 Dec 22. pii: 10.1038/s41589-021-00931-2. doi:, 10.1038/s41589-021-00931-2. PMID:34937911 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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