Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes

Abstract

Unique, three-dimensional structures have been determined for Escherichia coli small subunits, large Subunits and monomeric ribosomes by electron microscopy of ribosomes and subunits and of antibody-labeled ribosomes and subunits. Small subunits orient on the carbon substrate with their long axes parallel to the plane of the carbon. In these projections the subunit is divided into a onethird and a two-thirds portion by a region of accumulated negative stain similar to that observed in eukaryotic small subunits. Four characteristic views, or projections, are readily recognized and correspond to orientations of approximately −40 °, 0 °, +50 ° and +110 ° about the long axis of the subunit. Three of these have been described (Lake et al., 1974a; Lake & Kahan, 1975). The two most distinctive views are a quasi-symmetric view (0 °) that is characterized by an approximate line of mirror symmetry that coincides with the long axis of the subunit, and an asymmetric view (110 °) that is characterized by a concave and a convex subunit boundary. In the asymmetric projection, a platform or ledge is viewed “face-on”. The platform is attached to the lower two-thirds of the subunit just below the one-third/two-thirds partition. It is separated from the upper one-third of the subunit at the level of the partition and above the partition it forms a cleft approximately 30 to 40 Å wide, which has been suggested as the site of the codon-anticodon interaction (Lake & Kahan, 1975). Four characteristic views are presented for the large subunit. The most prominent of these, the quasi-symmetric view (θ = 90 °, φ = 0 °), is distinguished by a central protuberance located on a line of approximate mirror symmetry. The central protuberance is surrounded by projecting features inclined at about 50 ° on both sides of it. The smaller of these projections is rod-like, about 40 Å wide and approximately 100 Å long. The feature projecting from the other side of the central protuberance is shorter, more blunt and wider than the rod-like appendage. In another view approximately orthogonal to the quasi-symmetric projection, the asymmetric projection (θ = 10 °, φ = 90 °), the subunit profile is distinguished by a convex lower edge and an upper boundary which is indented by a notch. The subunit is separated, in projection, by the notch into two unequal regions. The smaller region comprises about 20% of the total projected density and consists of the central protuberance and the rod-like appendage. The profiles observed in fields of monomeric 70 S ribosomes result from superpositions of the 30 S and 50 S profiles. Two major views are observed, an overlap and a non-overlap view, corresponding to whether or not the profile of the small subunit overlaps that of the large subunit in the 70 S profile. The small subunit is oriented in the monomeric ribosome so that the platform is in contact with the large subunit. The central protuberance of the large subunit overlaps part of the upper one-third of the small subunit in the overlap view of 70 S ribosomes, although in three dimensions they are probably separated by 30 to 50 Å. A region of the small subunit comprising the platform, the cleft and part of the upper one-third, suggested to be the approximate binding site of IF3 and IF2 (Lake & Kalian, 1975), is located at the interface between the large and small subunits, in a region of the small subunit that is close to, but probably not in physical contact with, the large subunit.