1NTB

2.9 A crystal structure of Streptomycin RNA-aptamer complex

Summary for 1NTB

• Entry DOI: 10.2210/pdb1ntb/pdb
• Related: 1NTA
• Descriptor: 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3', 5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3', SODIUM ION, ... (6 entities in total)
• Functional Keywords: streptomycin rna-aptamer, magnesium form, rna
• Total number of polymer chains: 2
• Total formula weight: 13402.50

Authors

Tereshko, V.,Skripkin, E.,Patel, D.J. (deposition date: 2003-01-29, release date: 2003-05-13, Last modification date: 2024-04-03)

Primary citation

Tereshko, V.,Skripkin, E.,Patel, D.J.
Encapsulating Streptomycin within a small 40-mer RNA
CHEM.BIOL., 10:175-187, 2003

PubMed Abstract: We describe a 2.9 A X-ray structure of a complex between the aminocyclitol antibiotic streptomycin and an in vitro selected RNA aptamer, solved using the anomalous diffraction properties of Ba cations. The RNA aptamer, which contains two asymmetric internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and noncanonical pairs and triples. The streptomycin streptose ring is encapsulated by stacked arrays of bases from both loops at the elbow of the L-shaped RNA architecture. Specificity is defined by direct hydrogen bonds between all streptose functional groups and base edges that line the inner walls of the cylindrical binding pocket. By contrast, the majority of intermolecular interactions involve contacts to backbone phosphates in the published structure of streptomycin bound to the 16S rRNA.

PubMed: 12618190
DOI: 10.1016/S1074-5521(03)00024-3

Experimental method

X-RAY DIFFRACTION (2.9 Å)