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PDBsum entry 1c2w

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Ribosome PDB id
1c2w
Jmol
Contents
DNA/RNA

References listed in PDB file
Key reference
Title The 3d arrangement of the 23 s and 5 s rrna in the escherichia coli 50 s ribosomal subunit based on a cryo-Electron microscopic reconstruction at 7.5 a resolution.
Authors F.Mueller, I.Sommer, P.Baranov, R.Matadeen, M.Stoldt, J.Wöhnert, M.Görlach, M.Van heel, R.Brimacombe.
Ref. J Mol Biol, 2000, 298, 35-59. [DOI no: 10.1006/jmbi.2000.3635]
PubMed id 10756104
Abstract
The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure.
Figure 3.
Figure 3. The 3D arrangement of the double-helical elements of the 23 S and 5 S rRNA molecules in the 50 S subunit. The helices are represented as cylinders, numbered as in Figure 1. The colour-coding is: domain I, red; domain IIa, yellow; domain IIb, orange; domain III, green; domain IV, light blue; domain V, magenta; domain VI, dark blue; and 5 S rRNA grey-brown. (a) View of the structure from the L7/12 side of the subunit. (b) The same view as in (a), but with the layer of helices nearest to the reader removed. (c) View from the L1 side of the subunit. (d) The same view as in (c), but with the outer layer of helices removed as in (b).
Figure 10.
Figure 10. Distribution of the conserved core of the 23 S rRNA in the 50 S subunit. The helices of the conserved core (Figure 9) are displayed as cylinders, numbered and colour-coded as in Figure 3 and Figure 4. The EM density of the 50 S subunit is shown semi-transparent. (a) View from the L7/12 side of the subunit. (b) View from the interface side. (c) View from the L1 side. (d) View from the solvent side.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 35-59) copyright 2000.
Secondary reference #1
Title A new model for the three-Dimensional folding of escherichia coli 16 s ribosomal RNA. I. Fitting the RNA to a 3d electron microscopic map at 20 a.
Authors F.Mueller, R.Brimacombe.
Ref. J Mol Biol, 1997, 271, 524-544. [DOI no: 10.1006/jmbi.1997.1210]
PubMed id 9281424
Full text Abstract
Figure 2.
Figure 2. Overall features of the 16 S rRNA model. (a) Stereo view of the 16 S rRNA in the 70 S ribosome, viewed from the L7/L12 side (cf. [Stark et al 1997]). The 16 S molecule is colour coded as described in the text. The A and P site tRNAs are represented by the light blue and green tube models, respectively. (b) Stereo view of the 16 S rRNA in the 30 S subunit, viewed from the solvent side of the latter. The colour coding is as in (a). (c) The double helical elements of the 16 S rRNA in the 30 S subunit; a stereo view from the interface side of the subunit. The rRNA domains are coloured 5′ dark blue, central red, 3′ light blue, 3′-minor yellow.
Figure 7.
Figure 7. Stereo views of details of the central domain of the 16 S rRNA. (a) Helices 19, 20, 25, 26, 26a and 26t in the EM contour. The orientation is the same as that in Figure 4(a). (b) Helices 20, 22, 23 and 24, together with cross-link V (Figure 1) in the EM contour. The cross-link (nucleotides 693 to 696:794) is denoted by the ball-and-stick nucleotides. The orientation is similar to that in (a).
The above figures are reproduced from the cited reference with permission from Elsevier
Secondary reference #2
Title A new model for the three-Dimensional folding of escherichia coli 16 s ribosomal RNA. Ii. The RNA-Protein interaction data.
Authors F.Mueller, R.Brimacombe.
Ref. J Mol Biol, 1997, 271, 545-565. [DOI no: 10.1006/jmbi.1997.1211]
PubMed id 9281425
Full text Abstract
Figure 4.
Figure 4. (a) Protein S7, with interaction sites in rRNA helices 28, 29, 30.1, 41, 42 and 43. Orientation as for Figure 3(d). (b) Protein S9, with sites in helices 30, 38, 39 and 41. Orientation similar to (a) or Figure 3(d). (c) Protein S19, with sites in helices 28, 30, 31, 32, 33, 33a, 34.1, 42.2 and 43. Orientation as for Figure 3(c). See the text for details.
Figure 7.
Figure 7. (a) Protein S8, with interaction sites in helices 19, 20, 21, 24.1, 25, 26a and 26t. Orientation as for Figure 3(a). (b) Protein S15, with sites in helices 20.2, 22 and 23a. Orientation as in (a) or Figure 3(a). (c) Protein S11, with sites in helices 23, 24 and 25. Orientation as in (a) or Figure 3(a)(close-up view).
The above figures are reproduced from the cited reference with permission from Elsevier
Secondary reference #3
Title A new model for the three-Dimensional folding of escherichia coli 16 s ribosomal RNA. Iii. The topography of the functional centre.
Authors F.Mueller, H.Stark, M.Van heel, J.Rinke-Appel, R.Brimacombe.
Ref. J Mol Biol, 1997, 271, 566-587. [DOI no: 10.1006/jmbi.1997.1212]
PubMed id 9281426
Full text Abstract
Figure 4.
Figure 4. Foot-print sites to A and P site tRNA. The A and P site tRNAs are shown as pale blue and green backbone models, respectively, with the mRNA codons at the A and P sites as a white backbone model. (a) The 16 S rRNA helices 18.2 and 18t, and 44.1 to 44.5, with the A site foot-prints (Table 3) high-lighted as pale blue ball-and-stick nucleotides. (b) The 16 S rRNA helices 18.2 and 18t, 23, 24.3, 28, 29, 31, 43 and 44.1 to 44.5, with the P site foot-prints as green ball-and-stick nucleotides.
Figure 6.
Figure 6. (a) Foot-print sites to IF-1, and mutation sites causing translational suppression (cf. Table 3). The 16 S rRNA helices 18.2, 18t, 34 and 44.1 to 44.5 are displayed, with coloured ball-and-stick nucleotides denoting IF-1 foot-print sites (purple) and suppression sites in helices 18 and 34 (yellow and orange, respectively). (b) Mutation and foot-print sites for antibiotics. The 16 S rRNA helices 1, 2, 3, 18, 19, 27 and 34 are shown, with ball-and-stick nucleotides denoting streptomycin sites (yellow), tetracycline (red) and spectinomycin (purple). In (a) and (b) the A site tRNA is shown as a pale blue tube model.
The above figures are reproduced from the cited reference with permission from Elsevier
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