4KZE
Crystal structure of an RNA aptamer in complex with Fab
Summary for 4KZE
| Entry DOI | 10.2210/pdb4kze/pdb |
| Related | 3IVK 4KZD |
| Descriptor | BL3-6 Fab antibody, heavy chain, BL3-6 Fab antibody, light chain, RNA (84-MER), ... (6 entities in total) |
| Functional Keywords | g-quadruplex, fluorescence, fluorophore binding, immune system-rna complex, immune system/rna |
| Biological source | Mus musculus (mouse) More |
| Total number of polymer chains | 3 |
| Total formula weight | 75570.04 |
| 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: 2014-07-30) |
| 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 Cited by 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: 24952597DOI: 10.1038/nchembio.1561 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.404 Å) |
Structure validation
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