THE 3-DIMENSIONAL STRUCTURES OF 2 COMPLEXES BETWEEN RECOMBINANT MS2 CAPSIDS AND RNA OPERATOR FRAGMENTS REVEAL SEQUENCE-SPECIFIC PROTEIN-RNAINTERACTIONS

Crystal structures of two complexes between recombinant MS2 capsids an d RNA operator fragments have been determined at 2.7 Angstrom resoluti on. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid an d it acts as a translational repressor by binding with high specificit y to a unique site on the RNA, a single stem-loop structure, containin g the initiation codon of the gene for the viral replicase. Tn order t o determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with th e surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 51 side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, a nd with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at p osition -5 increases the affinity of the RNA to the dimer significantl y. The complex with RNA stem-loop having cytosine at this position dif fers from that of the wild-type complex mainly by having one extra int ramolecular RNA interaction and one extra water-mediated hydrogen bond . (C) 1997 Academic Press Limited.