4KZD

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

Summary for 4KZD

• Entry DOI: 10.2210/pdb4kzd/pdb
• Related: 3IVK 4KZE
• Related PRD ID: PRD_900003
• Descriptor: BL3-6 Fab antibody, heavy chain, BL3-6 Fab antibody, light chain, RNA (84-MER), ... (8 entities in total)
• Functional Keywords: g-quadruplex, fluorescence, fluorophore binding, in vitro, immune system-rna complex, immune system/rna
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 3
• Total formula weight: 76086.59

Authors

Huang, H.,Suslov, N.B.,Li, N.,Koldobskaya, Y.,Rice, P.A.,Piccirilli, J.A. (deposition date: 2013-05-29, release date: 2014-06-18, Last modification date: 2023-09-20)

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 (2.186 Å)