4Q9R

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

Summary for 4Q9R

• Entry DOI: 10.2210/pdb4q9r/pdb
• Related: 4KZD 4KZE 4Q9Q
• Descriptor: Fab BL3-6, HEAVY CHAIN, Fab BL3-6, LIGHT CHAIN, Spinach RNA aptamer, ... (6 entities in total)
• Functional Keywords: g-quadruplex, fluorescence, fluorophore, rna-immune system complex, rna/immune system
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 3
• Total formula weight: 74679.73

Authors

Huang, H.,Suslov, N.B.,Li, N.-S.,Shelke, S.A.,Evans, M.E.,Koldobskaya, Y.,Rice, P.A.,Piccirilli, J.A. (deposition date: 2014-05-01, release date: 2014-06-18, Last modification date: 2024-11-27)

Primary citation

Huang, H.,Suslov, N.B.,Li, N.S.,Shelke, S.A.,Evans, M.E.,Koldobskaya, Y.,Rice, P.A.,Piccirilli, J.A.
A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol., 10:686-691, 2014

PubMed Abstract: Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.

PubMed: 24952597
DOI: 10.1038/nchembio.1561

Experimental method

X-RAY DIFFRACTION (3.12 Å)