J. Mol. Biol. (1975) 91, 101-120 A Neutron Scattering Study of the Distribution of Protein and RNA in the 30 S Ribosomal Subunit of Escherichia coli PETER B. MOORE, DONALD M. ENGELMAN Department of Molecular Biophysics and Biochemistry Yale University, New Haven, Corm. 06520, U.S.A. AND BENNO P. SCHOENBORN Departmeti of Biology Brookhaven Notional Laboratory, Upton, L.I., N.Y. 11973, U.S.A. (Received 16 August 1974) The radii of gyration of the RNA and protein distributions of the 30 S subunit from Escherichia coli have been measured by neutron scattering experiments on the intact subunit. In addition the radius of gyration of the whole structure has been found, permitting estimation of the distance between the centers of mass of the RNA and protein distributions in the subunit. The results indicate that the radius of gyration of the protein parts is 73*7* 1.2 A, while that of the RNA is 67*2-j= 2-2 A. The radius of gyration of the whole particle is 71.4kO.6 A giving a 17.1+ g*” - 10.9 A separation between the protein and RNA centers of mass. Corres- ponding figures for the 50 S subunit are 73.4k2.0 A, 72*5f 1.5 A, 7%O&O.95 A, and 57*7& 10 A (Moore et al., 1974). Thus it appears that the two subunits differ substantially in overall organization. 1. Introduction The spatial organization of the proteins and RNA molecules which combine to form the ribosome is in many respects a paradigm of the next level of structure beyond single protein molecules. The size of objects of this class and the absence of crystals in many cases put these objects beyond the reach of conventional structural tech- niques. Consequently, a number of novel approaches have been proposed recently for their study. At least four of these are currently being applied to ribosomal structure: electron microscopic localization of specific antibody binding sites (Wabl, 1973,1974), energy transfer measurements (Cantor et al., 1974), crosslinking (Bickle et al., 1972; Chang t Blaks, 1972; Lutter et al., 1972), and neutron scattering (Engelman & Moore, 1972; Moore et al., 1974). In this paper we describe experiments using small-angle neutron scattering measure- ments of the 30 S ribosomal subunit to obtain radii of gyration for the protein and RNA mass distributions within the particle, as well as the radius of gyration of the whole structure. Each radius of gyration, R, is the second moment of the scattering mass distribution in question referred to its own center of mass, or c v? Ra=-, 2% 101