7eom | pdb_00007eom

Crystal structure of the Pepper aptamer in complex with HBC508

spinqualitylabelsall models 7eom, resolution 2.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7eom is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GTP, J8R, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G.U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization. Structure-based investigation of fluorogenic Pepper aptamer.,Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A Nat Chem Biol. 2021 Dec;17(12):1289-1295. doi: 10.1038/s41589-021-00884-6. Epub, 2021 Nov 1. PMID:34725509 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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