PDBsum entry 2rdo

Ribosome

PDB id: 2rdo

Contents

Protein chains

94 a.a.*

267 a.a.*

209 a.a.*

201 a.a.*

178 a.a.*

176 a.a.*

140 a.a.*

121 a.a.*

144 a.a.*

136 a.a.*

127 a.a.*

117 a.a.*

114 a.a.*

117 a.a.*

103 a.a.*

110 a.a.*

99 a.a.*

102 a.a.*

84 a.a.*

63 a.a.*

58 a.a.*

70 a.a.*

56 a.a.*

54 a.a.*

46 a.a.*

64 a.a.*

38 a.a.*

141 a.a.*

149 a.a.*

223 a.a.*

684 a.a.*

185 a.a.*

DNA/RNA

* C-alpha coords only

References listed in PDB file

Key reference

Title

Specific interaction between ef-G and rrf and its implication for gtp-Dependent ribosome splitting into subunits.

Authors

N.Gao, A.V.Zavialov, M.Ehrenberg, J.Frank.

Ref.

J Mol Biol, 2007, 374, 1345-1358. [DOI no: 10.1016/j.jmb.2007.10.021]

PubMed id

17996252

Abstract

After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF-containing posttermination ribosome triggers an interdomain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9-A (Fourier shell correlation cutoff of 0.5) cryo-electron microscopy map of a 50S x EF-G x guanosine 5'-[(betagamma)-imido]triphosphate x RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the noncleavable GTP analogue guanosine 5'-[(betagamma)-imido]triphosphate. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in transfer RNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G's domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits.

Figure 1.
Fig. 1. Overview of the quasi-atomic model of the 50S·EF-G·GDPNP·RRF complex. (a) Stereo view of the quasi-atomic structure of the 50S·EF-G·GDPNP·RRF complex superimposed with the cryo-EM density map. (b) The same stereo view of the quasi-atomic structure only. (c) Surface representation of the cryo-EM density map. (d) Overview of the interactions between EF-G and RRF. Ribosomal proteins, rRNAs, EF-G, and RRF are painted in green, gray, red, and blue, respectively. The domains of EF-G are labeled as I–IV. The two domains of RRF are labeled as “tail” (domain I) and “head” (domain II). Landmarks: L7L12, L7/12 stalk; L1, L1 stalk; CP, central protuberance; arc, arc-like connection between EF-G and L7/L12 stalk base.

Figure 2.
Fig. 2. Interactions between EF-G domain III and the interdomain hinges of RRF. (a) The interactions between one loop of EF-G domain III (Lys422-Lys424) and one of the hinges (Thr106-Glu108) of RRF. (b) Interactions between the other loop of EF-G domain III (Glu450-Asn453) and the two hinges and their neighboring residues of RRF. The residue stretches participating in the interactions are painted in green and yellow for RRF and EF-G, respectively. Residues that involve very strong contacts (< 3 Å) are displayed as a stick model.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 374, 1345-1358) copyright 2007.

Secondary reference #1

Title

Structural insights into fusidic acid resistance and sensitivity in ef-G.

Authors

S.Hansson, R.Singh, A.T.Gudkov, A.Liljas, D.T.Logan.

Ref.

J Mol Biol, 2005, 348, 939-949. [DOI no: 10.1016/j.jmb.2005.02.066]

PubMed id

15843024

Figure 1.
Figure 1. Comparison of EF-G structures with H573A, T84A and G16V mutations. (a) Superimposition of the C^a traces from H573A EF-G (green), T84A (magenta) and G16V (yellow). (b) Zoom in on the box in (a) showing the significant local differences in the conformations of switch II and helix B[III]. The colour scheme is the same as for (a). (c) An all-atom representation of switch II in the "wild-type" conformation observed in mutant H573A. The importance of Phe90 and Pro85 for the hydrophobic core can clearly be seen. In all panels, the GDP molecules are shown in a ball-and-stick representation with carbon atoms coloured identically to the C^a traces. The Mg ions are shown as magenta spheres.

Figure 5.
Figure 5. Mapping of the most FA resistant mutants in EF-G. A cartoon representation of the EF-G H573A structure is shown in green. The side-chains of the six most FA resistant mutations are shown in all-atom representation with carbon atoms coloured blue. In decreasing order of FA resistance, these mutations are: Phe90Leu, His458Tyr, Asp435Asn, Gln117Leu, Thr437Ile and Gly453Ser.19 Most of these are located at or near the switch II and domain III interface.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Structures of the bacterial ribosome at 3.5 a resolution.

Authors

B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, J.H.Cate.

Ref.

Science, 2005, 310, 827-834. [DOI no: 10.1126/science.1117230]

PubMed id

16272117

Figure 6.
Fig. 6. Molecular interactions in the intersubunit bridges. (A) Contact between S13 and L5 in ribosome I. (B) Contact between S13 and L5 in ribosome II. Only the C traces for the proteins are shown, because protein side chains are not clear in the electron density of either ribosome. Residues that become inaccessible to solvent (44) are indicated in orange for L5 and in yellow for S13 and S19. The direction of view is indicated in the center. (C) Molecular interactions in bridge B3. (D) Molecular interactions in bridge B7a. (E) Molecular interactions in bridge B6. Waters modeled at the interface are shown as red spheres inside the water-accessible volume, green mesh. (F) Close approach of phosphates at the subunit interface near bridge B2c. Distances (in angstroms) between phosphate oxygens are marked.

Figure 7.
Fig. 7. Intersubunit bridges B2a and B4. (A) Minor-groove interactions between H69 and h44 and h45, broken down by region. Atoms within hydrogen-bonding distance, as mentioned in the text, are connected by dashed lines. (B) Molecular interactions in bridge B4. Protein S15 in the 30S subunit is in blue, with relevant side chains in green. The interaction is viewed from the left side of Fig. 5A (left) and from the right side of Fig. 5A (right). Electron density is visible for the side chain of Arg88 (R88) in ribosome II, but not in ribosome I. Other amino acid abbreviations: I, Ile; L, Leu; V, Val; A, Ala; Q, Gln.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #3

Title

Crystal structure of the ribosome recycling factor from escherichia coli.

Authors

K.K.Kim, K.Min, S.W.Suh.

Ref.

EMBO J, 2000, 19, 2362-2370. [DOI no: 10.1093/emboj/19.10.2362]

PubMed id

10811627

Figure 4.
Figure 4 Stereo C[ ]traces of the / domain in RRF superimposed onto those of the C-terminal domain in the arginine repressor (van Duyne et al., 1996). A total of 48 C[ ]atoms (residues 55–103) in RRF are used for overlapping the / domain of RRF (thick line) with the C-terminal domain of the arginine repressor (thin line). C[ ]positions of the first, last and every 20th residues in RRF are labeled.

Figure 5.
Figure 5 The detergent molecule bound in a hydrophobic cleft. (A) A simulated-annealed omit electron density map calculated at 2.3 Å resolution with the detergent molecule omitted was drawn near the detergent-binding cleft. The detergent and surrounding residues were also drawn. (B) A stick model of the detergent located on a cleft of RRF drawn by surface charge distribution with the program GRASP (Nicholls et al., 1991). The white color represents the hydrophobic surface. The red and blue colors represent negatively and positively charged surfaces, respectively. The positions of the hydrophobic residues contacting the detergent are shown. The atoms outside the simulated-annealed omit map are excluded from the detergent model.

The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd

Secondary reference #4

Title

Structure of the l1 protuberance in the ribosome.

Authors

A.Nikulin, I.Eliseikina, S.Tishchenko, N.Nevskaya, N.Davydova, O.Platonova, W.Piendl, M.Selmer, A.Liljas, D.Drygin, R.Zimmermann, M.Garber, S.Nikonov.

Ref.

Nat Struct Biol, 2003, 10, 104-108. [DOI no: 10.1038/nsb886]

PubMed id

12514741

Figure 2.
Figure 2. Structure of the RNA fragment and its interactions with the protein. a, Stereo view of the RNA fragment. The RNA is colored according to secondary structure, and the GCAA tetraloop is gray. b, Diagram of stacking interactions within the RNA fragment. Nucleotides that hydrogen bond with the protein are shown with a gray background. Domain coloring is the same as (b). c, Portions of base stacking scheme, with amino acids that hydrogen bond to the RNA as indicated.

Figure 3.
Figure 3. Representation of the L1 protuberance within the ribosome. a, Superposition of the RNA fragments from the present complex (blue) and from the 70S ribosome (gold). Similar positions of H76 and H77 in both models are seen. Incorporation of the L1 -RNA complex into the models of b, the 50S from the T. thermophilus 70S ribosome and c, the D. radiodurans 50S ribosomal subunit. Protein L1 (red) and the 23S rRNA fragment (dark blue) are from the L1 -RNA complex, and the 5S rRNA (light blue) and 23S rRNA (gold) are from the corresponding subunits.

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

Secondary reference #5

Title

Mechanism for the disassembly of the posttermination complex inferred from cryo-Em studies.

Authors

N.Gao, A.V.Zavialov, W.Li, J.Sengupta, M.Valle, R.P.Gursky, M.Ehrenberg, J.Frank.

Ref.

Mol Cell, 2005, 18, 663-674. [DOI no: 10.1016/j.molcel.2005.05.005]

PubMed id

15949441

Figure 5.
Figure 5. Interaction of RRF with EF-G and Its Implication for the Disassembly of the Posttermination Complex

Figure 6.
Figure 6. Comparison of Two RRF Conformations on the 70S Posttermination Complex

The above figures are reproduced from the cited reference with permission from Cell Press