7SZU

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6

Summary for 7SZU

• Entry DOI: 10.2210/pdb7szu/pdb
• Descriptor: RNA aptamer, BL3-6 Fab heavy chain, BL3-6 Fab light chain, ... (7 entities in total)
• Functional Keywords: fluorogenic, immune system-rna complex, immune system/rna
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 3
• Total formula weight: 69063.95

Authors

Rees, H.C.,Piccirilli, J.A. (deposition date: 2021-11-29, release date: 2022-07-06, Last modification date: 2023-10-18)

Primary citation

Rees, H.C.,Gogacz, W.,Li, N.S.,Koirala, D.,Piccirilli, J.A.
Structural Basis for Fluorescence Activation by Pepper RNA.
Acs Chem.Biol., 17:1866-1875, 2022

PubMed Abstract: Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.

PubMed: 35759696
DOI: 10.1021/acschembio.2c00290

Experimental method

X-RAY DIFFRACTION (2.24 Å)