Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron x-ray solution scattering

The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simul ated annealing algorithm. The free 5 S rRNA is a bent elongated molecule di splaying a compact central region and two projecting arms, similar to those of the tRNA The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yield ing a tentative model of the structure of the free 5 S rRNA in solution. It s comparison with the recent protein-RNA map in the ribosome (Svergun, D. I ., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates th at the 5 S rRNA becomes essentially more compact upon complex formation wit h specific ribosomal proteins, A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interaction s are possible in the bound molecule.