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

* Residue conservation analysis

* C-alpha coords only

PDB id:

2rdo

Name:

Ribosome

Title:

50s subunit with ef-g(gdpnp) and rrf bound

Structure:

5s ribosomal RNA. Chain: a. 23s ribosomal RNA. Chain: b. 50s ribosomal protein l25. Chain: v. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.

Source:

Escherichia coli. Organism_taxid: 562. Organism_taxid: 562

Authors:

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

Key ref:

N.Gao et al. (2007). Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits. J Mol Biol, 374, 1345-1358. PubMed id: 17996252 DOI: 10.1016/j.jmb.2007.10.021

Date:

24-Sep-07 Release date: 04-Mar-08

Protein chain

P68919  (RL25_ECOLI) -  Large ribosomal subunit protein bL25 from Escherichia coli (strain K12)

Seq: 94 a.a.

Struc: 94 a.a.

Protein chain

P60422  (RL2_ECOLI) -  Large ribosomal subunit protein uL2 from Escherichia coli (strain K12)

Seq: 273 a.a.

Struc: 267 a.a.

Protein chain

P60438  (RL3_ECOLI) -  Large ribosomal subunit protein uL3 from Escherichia coli (strain K12)

Seq: 209 a.a.

Struc: 209 a.a.

Protein chain

P60723  (RL4_ECOLI) -  Large ribosomal subunit protein uL4 from Escherichia coli (strain K12)

Seq: 201 a.a.

Struc: 201 a.a.

Protein chain

P62399  (RL5_ECOLI) -  Large ribosomal subunit protein uL5 from Escherichia coli (strain K12)

Seq: 179 a.a.

Struc: 178 a.a.

Protein chain

P0AG55  (RL6_ECOLI) -  Large ribosomal subunit protein uL6 from Escherichia coli (strain K12)

Seq: 177 a.a.

Struc: 176 a.a.

Protein chain

P0AA10  (RL13_ECOLI) -  Large ribosomal subunit protein uL13 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 140 a.a.

Protein chain

P0ADY3  (RL14_ECOLI) -  Large ribosomal subunit protein uL14 from Escherichia coli (strain K12)

Seq: 123 a.a.

Struc: 121 a.a.

Protein chain

P02413  (RL15_ECOLI) -  Large ribosomal subunit protein uL15 from Escherichia coli (strain K12)

Seq: 144 a.a.

Struc: 144 a.a.

Protein chain

P0ADY7  (RL16_ECOLI) -  Large ribosomal subunit protein uL16 from Escherichia coli (strain K12)

Seq: 136 a.a.

Struc: 136 a.a.

Protein chain

P0AG44  (RL17_ECOLI) -  Large ribosomal subunit protein bL17 from Escherichia coli (strain K12)

Seq: 127 a.a.

Struc: 127 a.a.

Protein chain

P0C018  (RL18_ECOLI) -  Large ribosomal subunit protein uL18 from Escherichia coli (strain K12)

Seq: 117 a.a.

Struc: 117 a.a.

Protein chain

P0A7K6  (RL19_ECOLI) -  Large ribosomal subunit protein bL19 from Escherichia coli (strain K12)

Seq: 115 a.a.

Struc: 114 a.a.

Protein chain

P0A7L3  (RL20_ECOLI) -  Large ribosomal subunit protein bL20 from Escherichia coli (strain K12)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

P0AG48  (RL21_ECOLI) -  Large ribosomal subunit protein bL21 from Escherichia coli (strain K12)

Seq: 103 a.a.

Struc: 103 a.a.

Protein chain

P61175  (RL22_ECOLI) -  Large ribosomal subunit protein uL22 from Escherichia coli (strain K12)

Seq: 110 a.a.

Struc: 110 a.a.

Protein chain

P0ADZ0  (RL23_ECOLI) -  Large ribosomal subunit protein uL23 from Escherichia coli (strain K12)

Seq: 100 a.a.

Struc: 99 a.a.

Protein chain

P60624  (RL24_ECOLI) -  Large ribosomal subunit protein uL24 from Escherichia coli (strain K12)

Seq: 104 a.a.

Struc: 102 a.a.

Protein chain

P0A7L8  (RL27_ECOLI) -  Large ribosomal subunit protein bL27 from Escherichia coli (strain K12)

Seq: 85 a.a.

Struc: 84 a.a.

Protein chain

P0A7M6  (RL29_ECOLI) -  Large ribosomal subunit protein uL29 from Escherichia coli (strain K12)

Seq: 63 a.a.

Struc: 63 a.a.

Protein chain

P0AG51  (RL30_ECOLI) -  Large ribosomal subunit protein uL30 from Escherichia coli (strain K12)

Seq: 59 a.a.

Struc: 58 a.a.

Protein chain

P0A7M9  (RL31_ECOLI) -  Large ribosomal subunit protein bL31 from Escherichia coli (strain K12)

Seq: 70 a.a.

Struc: 70 a.a.

Protein chain

P0A7N4  (RL32_ECOLI) -  Large ribosomal subunit protein bL32 from Escherichia coli (strain K12)

Seq: 57 a.a.

Struc: 56 a.a.

Protein chain

P0A7N9  (RL33_ECOLI) -  Large ribosomal subunit protein bL33 from Escherichia coli (strain K12)

Seq: 55 a.a.

Struc: 54 a.a.

Protein chain

P0A7P5  (RL34_ECOLI) -  Large ribosomal subunit protein bL34 from Escherichia coli (strain K12)

Seq: 46 a.a.

Struc: 46 a.a.

Protein chain

P0A7Q1  (RL35_ECOLI) -  Large ribosomal subunit protein bL35 from Escherichia coli (strain K12)

Seq: 65 a.a.

Struc: 64 a.a.

Protein chain

P0A7Q6  (RL36_ECOLI) -  Large ribosomal subunit protein bL36A from Escherichia coli (strain K12)

Seq: 38 a.a.

Struc: 38 a.a.

Protein chain

P0A7J7  (RL11_ECOLI) -  Large ribosomal subunit protein uL11 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 141 a.a.

Protein chain

P0A7R1  (RL9_ECOLI) -  Large ribosomal subunit protein bL9 from Escherichia coli (strain K12)

Seq: 149 a.a.

Struc: 149 a.a.

Protein chain

P0A7L0  (RL1_ECOLI) -  Large ribosomal subunit protein uL1 from Escherichia coli (strain K12)

Seq: 234 a.a.

Struc: 223 a.a.

Protein chain

P0A6M8  (EFG_ECOLI) -  Elongation factor G from Escherichia coli (strain K12)

Seq: 704 a.a.

Struc: 684 a.a.

Protein chain

P0A805  (RRF_ECOLI) -  Ribosome-recycling factor from Escherichia coli (strain K12)

Seq: 185 a.a.

Struc: 185 a.a.

DNA/RNA chains

G-C-C-U-G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A-U- 117 bases

G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2841 bases

Enzyme reactions

• Enzyme class 2: Chains V, C, D, E, F, G, J, K, L, M, N, O, P, Q, R, S, T, U, W, X, Y, Z, 0, 1, 2, 3, 4, I, H, 9, 8: E.C.?
• Enzyme class 3: Chain 7: E.C.3.6.5.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/j.jmb.2007.10.021

J Mol Biol 374:1345-1358 (2007)

PubMed id: 17996252

Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.