Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Abstract

In considering the structure of the 30S subunit of the Escherichia coli ribosome, we have assumed that: (l) all or almost all the proteins within the 30S particle are compact and globular, as recently shown for the isolated proteins S4, S7, S8, S15, and S16 in solution [Serdyuk, I. N., Zaccai, G. & Spirin, A. S. (1978) In recent years, the technique of chemical crosslinking of neighboring proteins by bifunctional reagents and measurements of the distances between deuterated or fluorescent-labeled proteins by using neutron scattering or energy transfer techniques, respectively, have contributed much to the knowledge of the protein topography in ribosomal particles and especially in the ribosomal 30S subunit of Escherichia coli. From these and a number of less direct data, several models of the topography of ribosomal proteins in the 30S particle have been proposed (1)(2)(3)(4)(5)(6)(7)(8). Independently, the use of the immunoelectron microscopy technique has also led to two different models of the topography of ribosomal proteins on the surface of the 30S particle (9-12; see also ref. 13).However, two complications have hampered further progress. First, no information was available as to three-dimensional structure and morphology of the 16S RNA; this RNA is known to be a structural backbone for arrangement of ribosomal proteins. Second, immunoelectron microscopy (9, 10) and neutron scattering (14, 15) data on proteins within the 30S subunit, as well as some physical measurements of isolated ribosomal proteins (16-21), have suggested strongly elongated or very expanded shapes of many ribosomal proteins; this led to ambiguity in interpretation of the results on chemical crosslinking, energy transfer, etc.Most recently, a specific compact conformation of the 16S RNA has been visualized by electron microscopy (22). On the other hand, a number of ribosomal proteins, such as S4, S7, S8, S15, and S16, have been reinvestigated and found to be compact globular proteins with cooperative tertiary structures (23)(24)(25). Based on these new results and using the numerous data reported on mutual arrangement (topography) of ribosomal proteins, we have constructed a model of the quaternary structure of the ribosomal 30S particle and then checked it by neutron and x-ray scattering experiments.MODEL CONSTRUCTION Initial Assumptions. In constructing the model, we have adhered to the size and the asymmetric three-dimensional structure of the ribosomal 30S subunit first deduced by one of us from electron microscopy of freeze-dried and shadow-cast samples of the particles (26). Morphologically, the 30S particle was found to be subdivided into a "head," a "body," and a side "bulge" (Fig. 1). A similar subdivision of the 30S particles, with a side "platform," was reported also by Lake and Kahan (11) and Lake (27) on the basis of electron microscopy of negatively stained samples.We have proceeded from two principal assumptions: (i) RNA within the 30S particle has a specific V-like or Y-like conformation (Fig. 1), as it is visu...

Solution scattering structural analysis of the 70 s Escherichia coli ribosome by contrast variation. II † . A model of the ribosome and its RNA at 3.5 nm resolution 1 †Paper I in this series is the accompanying paper, Svergun et al. (1997) 1Edited by M. F. Moody

“…This argument does not seem to hold, since the R g TP30 evaluated from the triangulation map without S1 is 6.34 nm and thus not signi®-cantly different from that of the entire moiety. Our model displays a much better agreement with the model of the 30 S subunit proposed by Spirin et al (1979), which combined the protein positions with the V-shaped rRNA model by Vasiliev et al (1978). As seen from Figure 9(b), most of the proteins in the map by Spirin et al (1979) are positioned inside the gap between the envelope of the entire subunit and that of the rRNA moiety, whereas the lines representing the main axes of the V-shaped 16 S Solution Scattering Analysis of 70 S Ribosome.…”

The proteins of donor tRNA‐binding site of Escherichia coli ribosomes

“…The protein $9/S11 was shown earlier to be crosslinked with tRNA Phe in the ribosomal P-site after UV-irradiation (X = 254 nm) [14]. Using the method of reconstruction of ribosomal subunits from the proteins and rRNA after chemical modification of proteins it was shown that proteins S11 and $21 directly participate in tRNA-binding centre formation [20]. The proteins modified by photoreactive tRNA Phe analog in the ribosomal P-site according to our data are shaded.…”

“…Participation of the 50 S proteins L11, L13, L14 and L27 in P-site formation was shown using different tRNA derivatives containing reactive groups in the aminoacyl residue [17,18]. To date, several models are known of 30 S ribosomal subunit from E. coli obtained by different methods [19][20][21][22] for describing positions of proteins on the surface of the 30 S subunit. On the model in [21] which is the most complete for antigen determinants of the ribosomal proteins one can incorporate proteins found in the P-site according to our data into a compact group (see fig.4a).…”

“…On the model in [21] which is the most complete for antigen determinants of the ribosomal proteins one can incorporate proteins found in the P-site according to our data into a compact group (see fig.4a). Other models of the E. coli 30 S ribosomal subunit (proteins found in the P-site are shaded) are also represented in fig.4: the model of [22] derived from the data on bifunctional crosslinks between the ribosomal proteins (fig.4b); the model of [19] derived from immunoelectron microscopy (fig.4c); the model of [20] (fig.4d). It is evident that the model in [21 ] is the most convenient for the explanation of our data.…”

In vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30S ribosomal subunit

“…According to three-dimensional model of the 30S subunit, this protein is localized in the head region (2,3,24). Moreover, S13 has been shown to assemble directly with the 3Ј domain of the 16S RNA in stoichiometric amounts (6).…”