Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli

The crystal structure of an RNA dodecamer, r(GCGUCAGGUC^BrCG)/r(CGGAAGCAG^BrCGC), containing a fragment from the signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has been determined at 1.7 Å resolution with 21 666 independent reflections and an R_work and R_free of 20.1 and 22.5%, respectively. The structure exhibits a novel crystal packing pattern for RNA oligomer duplexes: one end of the duplex adopts the stacking interaction, while the other end adopts the abutting interaction in the minor groove. The symmetric loop of the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two different conformations of the A·C mismatch, a sheared G·G and a symmetrical G·A mismatch. These four mismatches present a unique surface for the abutting interaction. The involvement of the two A·C mismatches in the abutting interaction implies that these mismatches are the important sites for interaction with proteins. The conformation of the symmetric loop is greatly stabilized by hydrated metal ions, which display flexibility in adjusting their geometry and coordination in interaction with nucleic acids. Comparison with other crystal structures of fragments of 4.5S RNA indicates that the conformation of the symmetric loop is independent of the asymmetrical loop in domain IV.