The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability

The crystal and molecular structure of an RNA duplex corresponding to the h igh affinity Rev protein binding element (RBE) has been determined at 2.1-A ngstrom resolution. Four unique duplexes are present in the crystal, compri sing two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop con sisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. T he 12-mer strand has an A-form conformation, whereas the 14-mer strand is d istorted to accommodate the bulges and noncanonical base pairing. In contra st to the NMR model of the unbound RBE, an asymmetric: G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing a grees with the NMR structure in one structural variant, but forms a novel w ater-mediated pair in the other. A backbone flip and reorientation of the G -G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.