5BJP

Crystal structure of the Corn RNA aptamer in complex with DFHO, iridium hexammine soak

Summary for 5BJP

• Entry DOI: 10.2210/pdb5bjp/pdb
• Descriptor: RNA (36-MER), IRIDIUM ION, POTASSIUM ION, ... (7 entities in total)
• Functional Keywords: aptamer, fluorogenic rna, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 24536.98

Authors

Warner, K.D.,Song, W.,Filonov, G.S.,Jaffrey, S.R.,Ferre-D'Amare, A.R. (deposition date: 2016-08-21, release date: 2017-09-27, Last modification date: 2024-03-06)

Primary citation

Warner, K.D.,Sjekloca, L.,Song, W.,Filonov, G.S.,Jaffrey, S.R.,Ferre-D'Amare, A.R.
A homodimer interface without base pairs in an RNA mimic of red fluorescent protein.
Nat. Chem. Biol., 13:1195-1201, 2017

PubMed Abstract: Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures.

PubMed: 28945234
DOI: 10.1038/nchembio.2475

Experimental method

X-RAY DIFFRACTION (2.51 Å)