PDBsum entry: 1s1i

Ribosome

PDB id: 1s1i

Contents

Protein chains

213 a.a. *

244 a.a. *

359 a.a. *

256 a.a. *

222 a.a. *

161 a.a. *

119 a.a. *

178 a.a. *

165 a.a. *

165 a.a. *

131 a.a. *

194 a.a. *

146 a.a. *

147 a.a. *

120 a.a. *

141 a.a. *

97 a.a. *

131 a.a. *

53 a.a. *

77 a.a. *

115 a.a. *

143 a.a. *

109 a.a. *

78 a.a. *

59 a.a. *

52 a.a. *

91 a.a. *

73 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1s1i

Name:

Ribosome

Title:

Structure of the ribosomal 80s-eef2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 a cryo-em map. This file, 1s1i, contains 60s subunit. The 40s ribosomal subunit is in file 1s1h.

Structure:

5.8s/25s ribosomal RNA. Chain: 3. Other_details: represented by the analogous molecule of h. Marismortui taken from PDB entry 1ffk and supplemented with sequences from PDB entries 1mms, 1mzp and 1giy. 5s ribosomal RNA. Chain: 4. Other_details: represented by the analogous molecule of h. Marismortui taken from PDB entry 1ffk.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Biol. unit:

30mer (from PQS)

Resolution:

11.70Å R-factor: not given

Authors:

C.M.Spahn,M.G.Gomez-Lorenzo,R.A.Grassucci,R.Jorgensen, G.R.Andersen,R.Beckmann,P.A.Penczek,J.P.G.Ballesta,J.Frank

Key ref:

C.M.Spahn et al. (2004). Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J, 23, 1008-1019. PubMed id: 14976550 DOI: 10.1038/sj.emboj.7600102

Date:

06-Jan-04 Release date: 25-May-04

Protein chain

P0CX43  (RL1A_YEAST) -  60S ribosomal protein L1-A

Seq: 217 a.a.

Struc: 213 a.a.

Protein chain

P0CX45  (RL2A_YEAST) -  60S ribosomal protein L2-A

Seq: 254 a.a.

Struc: 244 a.a.

Protein chain

P14126  (RL3_YEAST) -  60S ribosomal protein L3

Seq: 387 a.a.

Struc: 359 a.a.

Protein chain

P49626  (RL4B_YEAST) -  60S ribosomal protein L4-B

Seq: 362 a.a.

Struc: 256 a.a.

Protein chain

P26321  (RL5_YEAST) -  60S ribosomal protein L5

Seq: 297 a.a.

Struc: 222 a.a.*

Protein chain

P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A

Seq: 244 a.a.

Struc: 161 a.a.

Protein chain

P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A

Seq: 256 a.a.

Struc: 119 a.a.

Protein chain

P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A

Seq: 191 a.a.

Struc: 178 a.a.

Protein chain

P41805  (RL10_YEAST) -  60S ribosomal protein L10

Seq: 221 a.a.

Struc: 165 a.a.

Protein chain

P0C0W9  (RL11A_YEAST) -  60S ribosomal protein L11-A

Seq: 174 a.a.

Struc: 165 a.a.

Protein chain

P0CX53  (RL12A_YEAST) -  60S ribosomal protein L12-A

Seq: 165 a.a.

Struc: 131 a.a.

Protein chain

P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A

Seq: 204 a.a.

Struc: 194 a.a.

Protein chain

P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A

Seq: 199 a.a.

Struc: 146 a.a.

Protein chain

P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A

Seq: 184 a.a.

Struc: 147 a.a.

Protein chain

P0CX49  (RL18A_YEAST) -  60S ribosomal protein L18-A

Seq: 186 a.a.

Struc: 120 a.a.

Protein chain

P0CX82  (RL19A_YEAST) -  60S ribosomal protein L19-A

Seq: 189 a.a.

Struc: 141 a.a.

Protein chain

Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A

Seq: 160 a.a.

Struc: 97 a.a.

Protein chain

P0CX41  (RL23A_YEAST) -  60S ribosomal protein L23-A

Seq: 137 a.a.

Struc: 131 a.a.

Protein chain

P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A

Seq: 155 a.a.

Struc: 53 a.a.

Protein chain

P04456  (RL25_YEAST) -  60S ribosomal protein L25

Seq: 142 a.a.

Struc: 77 a.a.

Protein chain

P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A

Seq: 127 a.a.

Struc: 115 a.a.

Protein chain

P02406  (RL28_YEAST) -  60S ribosomal protein L28

Seq: 149 a.a.

Struc: 143 a.a.*

Protein chain

P38061  (RL32_YEAST) -  60S ribosomal protein L32

Seq: 130 a.a.

Struc: 109 a.a.

Protein chain

P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A

Seq: 113 a.a.

Struc: 78 a.a.

Protein chain

P0CX84  (RL35A_YEAST) -  60S ribosomal protein L35-A

Seq: 120 a.a.

Struc: 59 a.a.

Protein chain

P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A

Seq: 88 a.a.

Struc: 52 a.a.

Protein chain

P0CX27  (RL44A_YEAST) -  60S ribosomal protein L42-A

Seq: 106 a.a.

Struc: 91 a.a.

Protein chain

P0CX25  (RL43A_YEAST) -  60S ribosomal protein L43-A

Seq: 92 a.a.

Struc: 73 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (8 terms)
• Biological process: ribosome biogenesis (7 terms)
• Biochemical function: structural constituent of ribosome (7 terms)

DOI no: 10.1038/sj.emboj.7600102

EMBO J 23:1008-1019 (2004)

PubMed id: 14976550

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, J.Frank.

ABSTRACT

An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.

Selected figure(s)

Figure 1.
Figure 1 A 11.7-Å-resolution cryo-EM map of the yeast 80S eEF2 sordarin complex. The cryo-EM map is shown (A) from the side; (B) from the top ; (C) from the 60S side, with 60S removed; and (D) from the 40S side, with 40S removed. The ribosomal 40S subunit is painted yellow, the 60S subunit blue and eEF2 red. Landmarks for the 40S subunit: b, body; bk, beak; h, head; lf, left foot; rf, right foot; pt, platform; sh, shoulder; sp, spur. Landmarks for the 60S subunit: CP, central protuberance; L1, L1 protuberance; SB, stalk base; St, stalk; H34, helix 34; H38, helix 38; SRL, sarcin -ricin loop.

Figure 6.
Figure 6 Model for tRNA movement during the translocation reaction. The coordinate transformations of the RSR, when applied to the A- and P-site bound tRNAs (A), result in hypothetical intermediates of the tRNAs during translocation (C, E) and a plausible trajectory for the path of the tRNAs from the A to the P and from the P to the E site. The corresponding state of the 40S subunit and its movements are shown in the cartoon in (B, D, F). The 40S subunit is shown on the left from the intersubunit side, and the head domain on the right from the top of the subunit. The crystallographically determined positions of the tRNAs in A (cyan), P (green) and E (purple) sites and an mRNA fragment (cyan) (Yusupov et al, 2001) are shown in (A) and are included in (C, E) as references painted in gray. (C) Shows the tRNAs in A (cyan) and P (green) sites after the coordinate transformation of the RSR for the body/platform domains of the 40S subunit (D) has been applied. The rotation of the 40S subunit is indicated by arrows, and the rotation axis at h27 of 18S rRNA by a star (D). The outline of the untransformed 40S (B) is included in (D) by the red line. The tRNA positions are further transformed (E) according to the additional movement of the head domain (F). This rotation occurs around a rotation axis through the neck of the 40S subunit (indicated by a star in (F)). The red line in (F) indicates the outline of the 40S subunit in (D).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1008-1019) copyright 2004.

Figures were selected by the author.