8jy0

Crystal structure of RhoBAST complexed with TMR-DN

spinqualitylabelsall models 8jy0, resolution 2.75Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8jy0 is a 6 chain structure with sequence from Homo sapiens and Artificial sequences. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.75Å Ligands: GDP, MG, PGE, V7U, V8C Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function M0R2B8_HUMAN Publication Abstract from PubMed The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.,Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X Nat Commun. 2024 May 17;15(1):4206. doi: 10.1038/s41467-024-48478-9. PMID:38760339 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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