3EGZ

Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch

Summary for 3EGZ

• Entry DOI: 10.2210/pdb3egz/pdb
• Descriptor: U1 small nuclear ribonucleoprotein A, Tetracycline aptamer and artificial riboswitch, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: tetracycline, aptamer, riboswitch, antibiotic, rna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 2
• Total formula weight: 33252.88

Authors

Xiao, H.,Edwards, T.E.,Ferre-D'Amare, A.R. (deposition date: 2008-09-11, release date: 2008-10-28, Last modification date: 2024-10-30)

Primary citation

Xiao, H.,Edwards, T.E.,Ferre-D'Amare, A.R.
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch
Chem.Biol., 15:1125-1137, 2008

PubMed Abstract: The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.

PubMed: 18940672
DOI: 10.1016/j.chembiol.2008.09.004

Experimental method

X-RAY DIFFRACTION (2.2 Å)