PDBsum entry 1ibm

Ribosome

PDB id: 1ibm

Contents

Protein chains

234 a.a. *

206 a.a. *

208 a.a. *

150 a.a. *

101 a.a. *

155 a.a. *

138 a.a. *

127 a.a. *

98 a.a. *

119 a.a. *

124 a.a. *

118 a.a. *

60 a.a. *

88 a.a. *

83 a.a. *

104 a.a. *

73 a.a. *

87 a.a. *

99 a.a. *

24 a.a. *

DNA/RNA

Metals

_MG ×120

_ZN ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Recognition of cognate transfer RNA by the 30s ribosomal subunit.

Authors

J.M.Ogle, D.E.Brodersen, W.M.Clemons, M.J.Tarry, A.P.Carter, V.Ramakrishnan.

Ref.

Science, 2001, 292, 897-902. [DOI no: 10.1126/science.1060612]

PubMed id

11340196

Abstract

Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.

Figure 2.
Fig. 2. Complex of the 30S subunit with mRNA from a U[6] hexanucleotide and a cognate tRNA-ASL. (A) Overview of the complex. The 50S interface side of the 30S subunit is facing the reader, and important elements have been given standard colors that are used throughout the figures, namely, ASL at the A site (gold), codon from the U[6] hexanucleotide at the A site (purple), 3' end of 16S RNA that mimics mRNA at the P site (green), P site tRNA mimic introduced by helix 6 from a neighboring molecule (dark blue), and protein S12 (tan). (B) Stereo view showing details of the A and P sites, colored as in (A), with, in addition, helix 44 (cyan, right), helix 34 (blue, left), 530 loop (green, left), and paromomycin (yellow sticks, within helix 44). The hydrogen bonds responsible for the codon-anticodon interaction at both the A and P sites are shown as red lines.

Figure 3.
Fig. 3. Stereo views showing interactions of the ribosome with the codon-anticodon base pairs. The tightness of the interactions is shown by the semitransparent van der Waals surface. (A) In the first position, A1493 binds in the minor groove of the A36-U1 base pair. (B) In the second position, G530 and A1492 (both brown) act in concert to monitor the A35-U2 base pair. (C) The third (wobble) position, showing the G34-U3 base pair. C1054 stacks against G36 of the ASL. U3 interacts with G530, and indirectly through a Mg2+ ion (magenta) with C518 and residue Pro48 (E. coli Pro44) from protein S12 (gray). The base pair seems closer to Watson-Crick geometry. (D) The third position in the presence of paromomycin, with the expected GU wobble pair. The interactions with the ribosome are similar to those in (C).

The above figures are reprinted by permission from the AAAs: Science (2001, 292, 897-902) copyright 2001.

Secondary reference #1

Title

Structure of the 30s ribosomal subunit.

Authors

B.T.Wimberly, D.E.Brodersen, W.M.Clemons, R.J.Morgan-Warren, A.P.Carter, C.Vonrhein, T.Hartsch, V.Ramakrishnan.

Ref.

Nature, 2000, 407, 327-339. [DOI no: 10.1038/35030006]

PubMed id

11014182

Figure 4.
Figure 4: Structure of the 5' domain of 16S RNA. a, Stereo view of the entire 5' domain, with an inset on the right showing its location in the 30S subunit. The upper (b), middle (c) and lower (d) subdomains are shown separately next to corresponding parts of the secondary structure diagrams. The colours in the secondary structure diagrams match those in the structure in this and Figs 5 and 6.

Figure 6.
Figure 6: Structure of the 3' major and 3' minor domains of 16S RNA. a, Stereo view of the 3' major domain with inset showing its location in the 30S. b-d, The upper, middle and lower parts of the 3' major domain, with corresponding secondary structure diagrams. e, Stereo view of the 3' minor domain, with secondary structure diagram and inset showing its location in the 30S.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #2

Title

Functional insights from the structure of the 30s ribosomal subunit and its interactions with antibiotics.

Authors

A.P.Carter, W.M.Clemons, D.E.Brodersen, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan.

Ref.

Nature, 2000, 407, 340-348. [DOI no: 10.1038/35030019]

PubMed id

11014183

Figure 4.
Figure 4: Interaction of spectinomycin with the 30S ribosomal subunit. a, Difference Fourier maps showing the binding site of spectinomycin in helix 34. b, Chemical structure of spectinomycin, showing interactions of the various groups with specific residues of 30S. c, The spectinomycin-binding site, showing its location at a pivotal point in the head of the 30S subunit. d, Inset showing spectinomycin in a space-filling model, and the location of its binding site on the 30S.

Figure 5.
Figure 5: Interaction of streptomycin with the 30S ribosomal subunit. a, Difference Fourier maps showing the binding site of streptomycin. Mutations in ribosomal protein S12 that confer resistance are shown in red. b, Chemical structure of streptomycin, showing interactions of the various groups with specific residues of the ribosome. c, The streptomycin-binding site, showing its interaction with H27, the 530 loop (H18), H44 and ribosomal protein S12. d, A view of the 30S showing streptomycin in a space-filling model, and the surrounding RNA and protein elements.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd