PDBsum entry 1hr0

Ribosome

PDB id: 1hr0

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. *

125 a.a. *

60 a.a. *

88 a.a. *

83 a.a. *

104 a.a. *

73 a.a. *

80 a.a. *

99 a.a. *

24 a.a. *

71 a.a. *

DNA/RNA

Metals

_MG ×65

_ZN ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of an initiation factor bound to the 30s ribosomal subunit.

Authors

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

Ref.

Science, 2001, 291, 498-501. [DOI no: 10.1126/science.1057766]

PubMed id

11228145

Abstract

Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.

Figure 1.
Fig. 1. Stereo views of electron density maps of the 30S-IF1 complex, showing a sheet in IF1. (A) [A]-weighted 2mF[o] DF[c] maps from an initial refinement in which no model for IF1 was included. (B) The corresponding maps after refinement with IF1.

Figure 2.
Fig. 2. Interaction of IF1 with the 30S subunit. (A) Close-up of the IF1 binding site, with IF1 in purple, helix 44 in cyan, the 530 loop in green, and protein S12 in orange. These colors are used throughout Figs. 2 and 3. (B) Overview showing the position of IF1 (purple) with respect to the 30S subunit (gray). H44, 530 loop, and S12 are colored as in (A). H, head; Bo, body; N, neck; Sh, shoulder; P, platform. (C) Overview of the 30S showing helix 44, S12, and the 530 loop as in (A), but with the A- P- and E-site tRNAs modeled as described in the text, in dark blue, orange, and yellow, respectively. Comparison with (B) shows that IF1 would block the binding of A-site tRNA. (D) Stereo pair showing A1492 and A1493 in H44 buried into protein pockets formed by IF1 and a combination of IF1 and S12.

The above figures are reprinted by permission from the AAAs: Science (2001, 291, 498-501) 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

Secondary reference #3

Title

Structure of a bacterial 30s ribosomal subunit at 5.5 a resolution.

Authors

W.M.Clemons, J.L.May, B.T.Wimberly, J.P.Mccutcheon, M.S.Capel, V.Ramakrishnan.

Ref.

Nature, 1999, 400, 833-840. [DOI no: 10.1038/23631]

PubMed id

10476960

Figure 4.
Figure 4 Stereo view of the three-way junction formed by helices 20, 21 and 22 of the central domain of 16S RNA. Inset (right) shows the structure in the context of the 30S subunit. Figure made with RIBBONS50.

Figure 5.
Figure 5 Stereo view of the interactions made by helix 27 of the central domain with helices 24 and 44 of 16S RNA. Inset (right) shows the elements in the whole 30S subunit. Figure made with RIBBONS50.

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