The structure of the HIV-1 RRE high affinity Rev binding site at 1.6 angstrom resolution

The crystal structure of a 28 nt RNA fragment containing the human immunode ficiency virus type 1 (HIV-1) Rev response element high affinity binding si te for Rev protein has been solved at 1.6 Angstrom resolution. The overall structure of the RRE helix is greatly distorted from A-form geometry by the presence of two purine-purine base-pairs and two single nucleotide bulges. G48 and G71 form a Hoogsteen-type asymmetric base-pair with G71 adopting a syn conformation. The non-canonical regions in the unliganded Rev response element molecule narrow the major groove width with respect to standard A- RNA. The Rev response element structure observed here represents a closed f orm of the Rev binding site and differs from conformations of the RNA obser ved previously by solution NMR studies. (C) 2000 Academic Press.