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Chapter 14 : Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures

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Abstract:

The structure of the bacterial ribosome, in particular that of , has been studied over a period of several decades with the help of a wide variety of biochemical and biophysical techniques. This chapter summarizes briefly how the 70S structure was derived and describes some of its principal features, with a view to convincing one that the authors are indeed involved in an ongoing transition from a ‘‘low-resolution model’’ to a ‘‘high resolution structure’’ of the ribosome. The cryo-EM reconstructions of 70S ribosomal complexes carrying tRNA are ideal substrates for combining electron density maps with biochemical models, because the tRNA molecules are directly visible in these reconstructions. The 50S subunit proteins for which X-ray or NMR structures are available include L1, the RNA-binding domain of L2, L6, the C-terminal domain of L7/12, L9, the RNA-binding domain of L11 both in isolated form and bound to a 23S rRNA fragment, L14, L22, L25, and L30. The CCA ends of the tRNAs at the P and A sites lie in the interface canyon, at the entrance to the peptide tunnel. The current versions of the 3-D structures that the authors have derived for the rRNA molecules are still far from perfect. The authors anticipate that they will be progressively improved as more data become available and as the resolution of the electron density maps increases.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14

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Figures

Image of Figure 1
Figure 1

Arrangement of rRNA in the 70S ribosome. The views are from the L7/12 side of the ribosome, and in the upper diagram the 16S rRNA (modeled into the 30S subunit) has been separated from the 23S and 5S rRNAs (modeled into the 50S subunit); the 16S rRNA is on the left. Only the double-helical elements of the rRNA molecules are shown, color coded according to secondary-structure domains. In the 16S rRNA, the 5′ domain is blue, the central domain is red, the 3′ domain is turquoise, and the 3′ minor domain is yellow. In the 23S rRNA, domain I is red, domain IIa is yellow, domain IIb is orange, domain III is green, domain IV is turquoise, domain V is magenta, and domain VI is blue-gray. The 5S rRNA is brown. In the lower (stereo) diagram, the same representation of the 16S, 23S, and 5S molecules is shown in situ within a semitransparent contour of the kirromycin-stalled 70S ribosome at 13 Å . The atomic structures of the P-site tRNA and of the EF-Tu–tRNA ternary complex are included as backbone tube models; the P-site tRNA is green, and the EF-Tu and tRNA moieties of the ternary complex are orange and yellow, respectively.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 2
Figure 2

Arrangement of proteins in the 30S subunit. The neutron map of is shown superimposed (see the text) on a transparent silhouette of the 30S subunit (excised from the 13-Å reconstruction of the 70S ribosome). The X-ray or NMR structures of proteins that have been modeled into the subunit via the 16S rRNA structure are shown as backbone tube models, and the corresponding protein spheres in the neutron map are rendered in the same colors. Protein numbers are shown for simplicity without the prefix S. The view is from the solvent side of the 30S subunit.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 3
Figure 3

Close-up view of proteins S5 and S8 in the semitransparent 30S subunit, together with appropriate elements of the 16S rRNA. The proteins are shown as backbone tube models (S5 is yellow; S8 is orange) as in Fig. 2, and the view is approximately the same as in that figure. Helical elements of the rRNA are numbered as in . Individual nucleotides and amino acids are color coded as follows. The magenta nucleotide in helix 21 and the corresponding magenta amino acid in S8 are those that are cross-linked together. Other cross-link sites from S8 in helix 21 are turquoise and white. The brown and yellow nucleotides in helices 21 and 25 are footprint sites for S8. The purple amino acid in S8 is cross-linked to the purple amino acid at the C terminus of S5. The red nucleotide (between helices 3 and 19) is the cross-link site from S5. The magenta and white nucleotides and amino acids (in S5) are spectinomycin sites, and the green and white nucleotides and amino acids are the corresponding streptomycin sites. See the text for references.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 4
Figure 4

Ribosomal components in the 50S subunit. Shown is a view from the L7/12 side of the semitransparent subunit. The atomic structures of EF-Tu, L25, and the RNA binding domain of L11 are displayed as backbone tube models colored orange, yellow, and magenta, respectively. The NMR structures of helices IV and V of the 5S rRNA, and of helix 95 of the 23S rRNA (the sarcin loop), are in black and white, and the modeled structure of helices 42, 43, and 44 of the 23S rRNA (the ”GTPase area”) is also included. Helix 42.4 is red-brown, helix 43 is green, helix 44 is purple, and the connecting strand between 43 and 44 (barely visible) is orange, as in the illustrations of the X-ray structure of . The remainder of helix 42 (i.e., 42.1 to 42.3) is black and white. The helix numbering is as in Mueller et al. (1999, ). See the text for further references.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 5
Figure 5

Positions of tRNA sites on the 50S subunit. The view is of the interface side of the 50S subunit, rendered as an opaque structure with prominent features (the L1 and L7/12 protuberances, the central protuberance [Cent. Prot.], and the A-site finger) marked. Density corresponding to the P-site tRNA and to the EF-Tu–tRNA complex has been removed. The tRNA molecules at the different sites and EF-Tu are displayed as backbone tube models, color coded as follows. EF-Tu is magenta, and tRNA in the EF-Tu–tRNA complex is blue. The A-site tRNA is white, the P-site tRNA is red, and the E site (corresponding approximately to the E2 site of ) is green. See the text for further details.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 6
Figure 6

Decoding area of the 16S rRNA, together with the relative locations of elements of the 23S rRNA. Helix 28 and part of 44 of the 16S rRNA are shown, with the nucleotides described in the NMR structure of highlighted in orange. Helices 69 and 80 are included from the 23S rRNA. The P-site tRNA and mRNA are displayed as backbone tube models (yellow and orange, respectively), in positions adapted from the model of , and the pre-A-site tRNA (in the EF-Tu– tRNA ternary complex) is similarly shown in green. Positions 34 of the P-site tRNA and C1400 of the 16S rRNA (which are cross-linked) are shown as red CPK nucleotides. Similarly, positions +4 of the mRNA and C1402 of the 16S rRNA are purple. Nucleotides 1492 and 1493 (footprint sites for A-site tRNA) are green, and nucleotide 1408 (footprint site for A-site tRNA and cross-link site to helix 69 in 23S rRNA) is turquoise. The CCA end of the P-site tRNA has been turned upwards (in accordance with the EM density), and the potential base pair from C74 to G2252 in helix 80 is indicated by the magenta CPK nucleotides. The lower part of the figure shows a stereo pair of the same structural elements.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 7
Figure 7

Path of mRNA through the 30S subunit. A close-up stereo view of the interface side of the (semitransparent) 30S subunit is shown. The P-site tRNA and protein S7 are displayed as backbone tube models, in blue-gray and green, respectively. The mRNA is displayed as a backbone tube model, with the upstream sequence red, the P-site codon blue-gray and the downstream region brown. Nucleotides at positions −1, −3, and −4 of the mRNA, which can be cross-linked to S7, are shown as red wireframe structures.

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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Image of Figure 8
Figure 8

Path of the nascent peptide through the 50S subunit. The 50S subunit, viewed from the L7/12 side, is displayed as an opaque structure with density elements cut away (leaving the dark brown ”scars”) to reveal the peptide tunnel. The EM density corresponding to the P-site tRNA has also been removed, and the P-site tRNA is shown as a red backbone tube model. The arrow indicates the path followed by the growing peptide chain, with the colored balls showing the sites on 23S rRNA that are cross-linked from the N termini of peptides with increasing minimum lengths, color coded as follows: red, position 2609 (3 amino acids); orange, position 1781 (4 amino acids); green, position 750 (6 amino acids); turquoise, position 1614 (12 or 25 amino acids; see ); magenta, position 91 (30 amino acids).

Citation: Brimacombe R, Greuer B, Mueller F, Osswald M, Rinke-Appel J, Sommer I. 2000. Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures, p 151-164. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch14
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