A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome

Neutron scattering exploits the enormous scattering difference between prot ons and deuterons. A set of 42 x-ray and neutron solution scattering curves from hybrid Escherichia coli ribosomes was obtained, where the proteins an d rRNA moieties in the subunits were either protonated or deuterated in all possible combinations. This extensive data set is analyzed using a novel m ethod. The volume defined by the cryoelectron microscopic model of Frank an d co-workers (Frank, J., Zhu, J., Penczek, P., Li, Y. H., Srivastava, S., V erschoor, A., Radermacher, NI,, Grassucci, R., Lata, R. K., and Agrawal, R, K. (1995) Nature 376, 441-444) is divided into 7890 densely packed spheres of radius 0.5 nm. Simulated annealing is employed to assign each sphere to solvent, protein, or rRNA moieties to simultaneously fit all scattering cu rves. Twelve independent reconstructions starting from random approximation s yielded reproducible results. The resulting model at a resolution of 3 nm represents the volumes occupied by rRNA and protein moieties at 95% probab ility threshold and displays 15 and 20 protein subvolumes in the 30 S and 5 0 S, respectively, connected by rRNA. 17 proteins with known atomic structu re can be tentatively positioned into the protein subvolumes within the rib osome in agreement with the results from other methods. The protein-rRNA ma p enlarges the basis for the models of the rRNA folding and can further hel p to localize proteins in high-resolution crystallographic density maps.