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PDBsum entry 1s1h
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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
1s1h

 

 

 

 

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Contents
Protein chains
819 a.a. *
185 a.a. *
188 a.a. *
178 a.a. *
149 a.a. *
150 a.a. *
127 a.a. *
139 a.a. *
97 a.a. *
125 a.a. *
118 a.a. *
131 a.a. *
29 a.a. *
65 a.a. *
76 a.a. *
80 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1s1h
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, 1s1h, contains 40s subunit. The 60s ribosomal subunit is in file 1s1i.
Structure: 18s ribosomal RNA. Chain: a. Other_details: modelled as analogous molecule of t. Thermophilus taken from PDB entry 1fjf. Elongation factor 2. Chain: t. Synonym: ef-2. 40s ribosomal protein s0-a. Chain: b.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932
Biol. unit: 70mer (from PQS)
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P32324  (EF2_YEAST) -  Elongation factor 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		842 a.a.
819 a.a.
Protein chain
Pfam   ArchSchema ?
P32905  (RSSA1_YEAST) -  40S ribosomal protein S0-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		252 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P05750  (RS3_YEAST) -  40S ribosomal protein S3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		240 a.a.
188 a.a.
Protein chain
Pfam   ArchSchema ?
O13516  (RS9A_YEAST) -  40S ribosomal protein S9-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		197 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P25443  (RS2_YEAST) -  40S ribosomal protein S2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		254 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P26783  (RS5_YEAST) -  40S ribosomal protein S5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		225 a.a.
150 a.a.
Protein chain
P04648  (RS22_YEAST) - 
Protein chain
P40213  (RS16_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P38701  (RS20_YEAST) -  40S ribosomal protein S20 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		121 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P06367  (RS14A_YEAST) -  40S ribosomal protein S14-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		137 a.a.
125 a.a.*
Protein chain
P32827  (RS23_YEAST) - 
Protein chain
P35271  (RS18_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P41058  (RS29B_YEAST) -  40S ribosomal protein S29-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		56 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P05756  (RS13_YEAST) -  40S ribosomal protein S13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		151 a.a.
65 a.a.
Protein chain
P26781  (RS11_YEAST) - 
Protein chain
Pfam   ArchSchema ?
Q01855  (RS15_YEAST) -  40S ribosomal protein S15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		142 a.a.
80 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1466 bases

 

 
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 an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22358840 T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, and R.Beckmann (2012).
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
  Nature, 482, 501-506.
PDB codes: 3j15 3j16
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
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21336521 M.Valle (2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
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21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
19691449 A.Fatehullah, C.Doherty, G.Pivato, G.Allen, L.Devine, J.Nelson, and D.J.Timson (2010).
Interactions of the 67 kDa laminin receptor and its precursor with laminin.
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21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
20419091 A.Neueder, S.Jakob, G.Pöll, J.Linnemann, R.Deutzmann, H.Tschochner, and P.Milkereit (2010).
A local role for the small ribosomal subunit primary binder rpS5 in final 18S rRNA processing in yeast.
  PLoS One, 5, e10194.  
20423979 C.J.Jang, and E.Jan (2010).
Modular domains of the Dicistroviridae intergenic internal ribosome entry site.
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20348448 C.Mary, A.Scherrer, L.Huck, A.K.Lakkaraju, Y.Thomas, A.E.Johnson, and K.Strub (2010).
Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein.
  RNA, 16, 969-979.  
20797628 F.Brandt, L.A.Carlson, F.U.Hartl, W.Baumeister, and K.Grünewald (2010).
The three-dimensional organization of polyribosomes in intact human cells.
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20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
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21057527 J.B.Munro, M.R.Wasserman, R.B.Altman, L.Wang, and S.C.Blanchard (2010).
Correlated conformational events in EF-G and the ribosome regulate translocation.
  Nat Struct Mol Biol, 17, 1470-1477.  
20159470 J.F.Flanagan, O.Namy, I.Brierley, and R.J.Gilbert (2010).
Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes.
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20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20385603 K.M.Lee, C.W.Yu, D.S.Chan, T.Y.Chiu, G.Zhu, K.H.Sze, P.C.Shaw, and K.B.Wong (2010).
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  Nucleic Acids Res, 38, 5206-5216.
PDB code: 2w1o
20670889 K.Y.Lo, Z.Li, C.Bussiere, S.Bresson, E.M.Marcotte, and A.W.Johnson (2010).
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.
  Mol Cell, 39, 196-208.  
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
20699223 N.Nemoto, C.R.Singh, T.Udagawa, S.Wang, E.Thorson, Z.Winter, T.Ohira, M.Ii, L.Valásek, S.J.Brown, and K.Asano (2010).
Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation.
  J Biol Chem, 285, 32200-32212.  
20686683 R.Potestio, C.Micheletti, and H.Orland (2010).
Knotted vs. unknotted proteins: evidence of knot-promoting loops.
  PLoS Comput Biol, 6, e1000864.  
20007716 T.Naganuma, N.Nomura, M.Yao, M.Mochizuki, T.Uchiumi, and I.Tanaka (2010).
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  J Biol Chem, 285, 4747-4756.
PDB code: 3a1y
20511136 X.Agirrezabala, and J.Frank (2010).
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  Hum Genomics, 4, 226-237.  
19854950 Y.Lustig, C.Wachtel, M.Safro, L.Liu, and S.Michaeli (2010).
'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target.
  Nucleic Acids Res, 38, e5.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19029250 B.S.Shin, J.R.Kim, M.G.Acker, K.N.Maher, J.R.Lorsch, and T.E.Dever (2009).
rRNA suppressor of a eukaryotic translation initiation factor 5B/initiation factor 2 mutant reveals a binding site for translational GTPases on the small ribosomal subunit.
  Mol Cell Biol, 29, 808-821.  
19628620 C.Hsiao, S.Mohan, B.K.Kalahar, and L.D.Williams (2009).
Peeling the onion: ribosomes are ancient molecular fossils.
  Mol Biol Evol, 26, 2415-2425.  
19536129 C.Ticu, R.Nechifor, B.Nguyen, M.Desrosiers, and K.S.Wilson (2009).
Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome.
  EMBO J, 28, 2053-2065.  
19539793 C.U.Hellen (2009).
IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry.
  Biochim Biophys Acta, 1789, 558-570.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19952110 D.M.Landry, M.I.Hertz, and S.R.Thompson (2009).
RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs.
  Genes Dev, 23, 2753-2764.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
20011513 G.Pöll, T.Braun, J.Jakovljevic, A.Neueder, S.Jakob, J.L.Woolford, H.Tschochner, and P.Milkereit (2009).
rRNA maturation in yeast cells depleted of large ribosomal subunit proteins.
  PLoS One, 4, e8249.  
19571367 I.Tinoco, and J.D.Wen (2009).
Simulation and analysis of single-ribosome translation.
  Phys Biol, 6, 25006.  
19717422 J.Fei, J.E.Bronson, J.M.Hofman, R.L.Srinivas, C.H.Wiggins, and R.L.Gonzalez (2009).
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.
  Proc Natl Acad Sci U S A, 106, 15702-15707.  
19239892 N.Sonenberg, and A.G.Hinnebusch (2009).
Regulation of translation initiation in eukaryotes: mechanisms and biological targets.
  Cell, 136, 731-745.  
19666721 N.Van Dyke, B.F.Pickering, and M.W.Van Dyke (2009).
Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation.
  Nucleic Acids Res, 37, 6116-6125.  
19223173 S.C.Blanchard (2009).
Single-molecule observations of ribosome function.
  Curr Opin Struct Biol, 19, 103-109.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
19417061 S.Shoji, N.M.Abdi, R.Bundschuh, and K.Fredrick (2009).
Contribution of ribosomal residues to P-site tRNA binding.
  Nucleic Acids Res, 37, 4033-4042.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18832371 A.Meskauskas, and J.D.Dinman (2008).
Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.
  Nucleic Acids Res, 36, 6175-6186.  
18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
  Nucleic Acids Res, 36, 6187-6198.  
17947322 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2008).
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
  Nucleic Acids Res, 36, D178-D183.  
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
  Biopolymers, 89, 565-577.  
18285480 J.Botet, M.Rodríguez-Mateos, J.P.Ballesta, J.L.Revuelta, and M.Remacha (2008).
A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin.
  Antimicrob Agents Chemother, 52, 1623-1629.  
18708582 J.Dong, J.S.Nanda, H.Rahman, M.R.Pruitt, B.S.Shin, C.M.Wong, J.R.Lorsch, and A.G.Hinnebusch (2008).
Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNA(Met) and AUG selection.
  Genes Dev, 22, 2242-2255.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
18644383 J.Sengupta, J.Nilsson, R.Gursky, M.Kjeldgaard, P.Nissen, and J.Frank (2008).
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
  J Mol Biol, 382, 179-187.
PDB codes: 3dny 3dwu
18957409 K.J.Webb, A.Laganowsky, J.P.Whitelegge, and S.G.Clarke (2008).
Identification of Two SET Domain Proteins Required for Methylation of Lysine Residues in Yeast Ribosomal Protein Rpl42ab.
  J Biol Chem, 283, 35561-35568.  
18951096 L.Garcia-Ortega, J.Stephen, and S.Joseph (2008).
Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
  Mol Cell, 32, 292-299.  
18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure, 16, 535-548.
PDB codes: 2zkq 2zkr
18462671 S.J.Moran, J.F.Flanagan, O.Namy, D.I.Stuart, I.Brierley, and R.J.Gilbert (2008).
The mechanics of translocation: a molecular "spring-and-ratchet" system.
  Structure, 16, 664-672.  
18765564 T.R.Webb, S.H.Cross, L.McKie, R.Edgar, L.Vizor, J.Harrison, J.Peters, and I.J.Jackson (2008).
Diphthamide modification of eEF2 requires a J-domain protein and is essential for normal development.
  J Cell Sci, 121, 3140-3145.  
18632761 T.V.Budkevich, A.V.El'skaya, and K.H.Nierhaus (2008).
Features of 80S mammalian ribosome and its subunits.
  Nucleic Acids Res, 36, 4736-4744.  
19081053 W.Zhang, M.Kimmel, C.M.Spahn, and P.A.Penczek (2008).
Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.
  Structure, 16, 1770-1776.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
17386264 A.Meskauskas, and J.D.Dinman (2007).
Ribosomal protein L3: gatekeeper to the A site.
  Mol Cell, 25, 877-888.  
17893680 A.Roguev, M.Wiren, J.S.Weissman, and N.J.Krogan (2007).
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.
  Nat Methods, 4, 861-866.  
17568775 A.Unbehaun, A.Marintchev, I.B.Lomakin, T.Didenko, G.Wagner, C.U.Hellen, and T.V.Pestova (2007).
Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing.
  EMBO J, 26, 3109-3123.  
17881742 C.Guarraia, L.Norris, A.Raman, and P.J.Farabaugh (2007).
Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon.
  RNA, 13, 1940-1947.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
  EMBO J, 26, 2421-2431.
PDB codes: 2p8w 2p8x 2p8y 2p8z
17283215 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2007).
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
  RNA, 13, 305-312.  
17308345 D.S.Chan, L.O.Chu, K.M.Lee, P.H.Too, K.W.Ma, K.H.Sze, G.Zhu, P.C.Shaw, and K.B.Wong (2007).
Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses.
  Nucleic Acids Res, 35, 1660-1672.  
17892487 G.Bartish, H.Moradi, and O.Nygård (2007).
Amino acids Thr56 and Thr58 are not essential for elongation factor 2 function in yeast.
  FEBS J, 274, 5285-5297.  
17569673 I.V.Rosado, D.Kressler, and J.de la Cruz (2007).
Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis.
  Nucleic Acids Res, 35, 4203-4213.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
17521420 J.L.Jiménez, B.Hegemann, J.R.Hutchins, J.M.Peters, and R.Durbin (2007).
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.
  Genome Biol, 8, R90.  
17434183 J.Nilsson, J.Sengupta, R.Gursky, P.Nissen, and J.Frank (2007).
Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments.
  J Mol Biol, 369, 429-438.  
17434125 L.A.Passmore, T.M.Schmeing, D.Maag, D.J.Applefield, M.G.Acker, M.A.Algire, J.R.Lorsch, and V.Ramakrishnan (2007).
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
  Mol Cell, 26, 41-50.  
17704133 M.Léger, D.Dulude, S.V.Steinberg, and L.Brakier-Gingras (2007).
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
  Nucleic Acids Res, 35, 5581-5592.  
17586816 N.Demeshkina, G.Hirokawa, A.Kaji, and H.Kaji (2007).
Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP.
  Nucleic Acids Res, 35, 4597-4607.  
17901157 O.Galkin, A.A.Bentley, S.Gupta, B.A.Compton, B.Mazumder, T.G.Kinzy, W.C.Merrick, M.Hatzoglou, T.V.Pestova, C.U.Hellen, and A.A.Komar (2007).
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5.
  RNA, 13, 2116-2128.  
17389391 R.J.Gilbert, Y.Gordiyenko, T.von der Haar, A.F.Sonnen, G.Hofmann, M.Nardelli, D.I.Stuart, and J.E.McCarthy (2007).
Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
  Proc Natl Acad Sci U S A, 104, 5788-5793.  
17082187 R.Søe, R.T.Mosley, M.Justice, J.Nielsen-Kahn, M.Shastry, A.R.Merrill, and G.R.Andersen (2007).
Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2.
  J Biol Chem, 282, 657-666.
PDB codes: 2e1r 2npf
17996708 S.Ferreira-Cerca, G.Pöll, H.Kühn, A.Neueder, S.Jakob, H.Tschochner, and P.Milkereit (2007).
Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins.
  Mol Cell, 28, 446-457.  
17349960 S.R.Connell, C.Takemoto, D.N.Wilson, H.Wang, K.Murayama, T.Terada, M.Shirouzu, M.Rost, M.Schüler, J.Giesebrecht, M.Dabrowski, T.Mielke, P.Fucini, S.Yokoyama, and C.M.Spahn (2007).
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
  Mol Cell, 25, 751-764.
PDB code: 2om7
17353896 T.F.Menne, B.Goyenechea, N.Sánchez-Puig, C.C.Wong, L.M.Tonkin, P.J.Ancliff, R.L.Brost, M.Costanzo, C.Boone, and A.J.Warren (2007).
The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast.
  Nat Genet, 39, 486-495.  
17327221 T.R.Porras-Yakushi, J.P.Whitelegge, and S.Clarke (2007).
Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily: identification of Rpl23ab methylation sites and recognition motifs.
  J Biol Chem, 282, 12368-12376.  
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
17925437 W.Li, and J.Frank (2007).
Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
  Proc Natl Acad Sci U S A, 104, 16540-16545.  
17064936 Y.Zhang, V.A.Kostyuchenko, and M.G.Rossmann (2007).
Structural analysis of viral nucleocapsids by subtraction of partial projections.
  J Struct Biol, 157, 356-364.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
  RNA, 12, 790-796.  
16682566 A.Raman, C.Guarraia, D.Taliaferro, G.Stahl, and P.J.Farabaugh (2006).
An mRNA sequence derived from a programmed frameshifting signal decreases codon discrimination during translation initiation.
  RNA, 12, 1154-1160.  
16929303 C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, and R.Beckmann (2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
  Nature, 443, 663-668.
PDB codes: 2iw3 2iwh 2ix3 2ix8
16307820 E.Jan (2006).
Divergent IRES elements in invertebrates.
  Virus Res, 119, 16-28.  
16777602 E.Z.Alkalaeva, A.V.Pisarev, L.Y.Frolova, L.L.Kisselev, and T.V.Pestova (2006).
In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3.
  Cell, 125, 1125-1136.  
16689644 H.Stark, and R.Lührmann (2006).
Cryo-electron microscopy of spliceosomal components.
  Annu Rev Biophys Biomol Struct, 35, 435-457.  
16973438 I.K.Ali, L.Lancaster, J.Feinberg, S.Joseph, and H.F.Noller (2006).
Deletion of a conserved, central ribosomal intersubunit RNA bridge.
  Mol Cell, 23, 865-874.  
16489185 J.S.Feinberg, and S.Joseph (2006).
Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation.
  RNA, 12, 580-588.  
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
  Annu Rev Biophys Biomol Struct, 35, 299-317.  
16890441 K.P.Hofmann, C.M.Spahn, R.Heinrich, and U.Heinemann (2006).
Building functional modules from molecular interactions.
  Trends Biochem Sci, 31, 497-508.  
17115051 M.Schüler, S.R.Connell, A.Lescoute, J.Giesebrecht, M.Dabrowski, B.Schroeer, T.Mielke, P.A.Penczek, E.Westhof, and C.M.Spahn (2006).
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
  Nat Struct Mol Biol, 13, 1092-1096.
PDB code: 2noq
16648468 N.J.Hung, and A.W.Johnson (2006).
Nuclear recycling of the pre-60S ribosomal subunit-associated factor Arx1 depends on Rei1 in Saccharomyces cerevisiae.
  Mol Cell Biol, 26, 3718-3727.  
16688178 O.Namy, S.J.Moran, D.I.Stuart, R.J.Gilbert, and I.Brierley (2006).
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.
  Nature, 441, 244-247.  
16950777 P.A.Ortiz, R.Ulloque, G.K.Kihara, H.Zheng, and T.G.Kinzy (2006).
Translation elongation factor 2 anticodon mimicry domain mutants affect fidelity and diphtheria toxin resistance.
  J Biol Chem, 281, 32639-32648.  
16406634 S.P.Yates, R.Jørgensen, G.R.Andersen, and A.R.Merrill (2006).
Stealth and mimicry by deadly bacterial toxins.
  Trends Biochem Sci, 31, 123-133.  
16053518 A.Liiv, D.Karitkina, U.Maiväli, and J.Remme (2005).
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
  BMC Mol Biol, 6, 18.  
16314511 A.Meskauskas, A.N.Petrov, and J.D.Dinman (2005).
Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis.
  Mol Cell Biol, 25, 10863-10874.  
16272117 B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, and J.H.Cate (2005).
Structures of the bacterial ribosome at 3.5 A resolution.
  Science, 310, 827-834.
PDB codes: 2avy 2aw4 2aw7 2awb
16314459 C.L.Shenvi, K.C.Dong, E.M.Friedman, J.A.Hanson, and J.H.Cate (2005).
Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
  RNA, 11, 1898-1908.  
16164560 C.Santos, and J.P.Ballesta (2005).
Characterization of the 26S rRNA-binding domain in Saccharomyces cerevisiae ribosomal stalk phosphoprotein P0.
  Mol Microbiol, 58, 217-226.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16257826 D.N.Wilson, and K.H.Nierhaus (2005).
Ribosomal proteins in the spotlight.
  Crit Rev Biochem Mol Biol, 40, 243-267.  
16014419 H.Gao, M.J.Ayub, M.J.Levin, and J.Frank (2005).
The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.
  Proc Natl Acad Sci U S A, 102, 10206-10211.  
  18074004 J.D.Dinman (2005).
5S rRNA: Structure and Function from Head to Toe.
  Int J Biomed Sci, 1, 2-7.  
15922593 J.Nilsson, and P.Nissen (2005).
Elongation factors on the ribosome.
  Curr Opin Struct Biol, 15, 349-354.  
15864315 M.Halic, T.Becker, J.Frank, C.M.Spahn, and R.Beckmann (2005).
Localization and dynamic behavior of ribosomal protein L30e.
  Nat Struct Mol Biol, 12, 467-468.
PDB code: 1ysh
16118050 M.Topf, and A.Sali (2005).
Combining electron microscopy and comparative protein structure modeling.
  Curr Opin Struct Biol, 15, 578-585.  
16214807 P.A.Ortiz, and T.G.Kinzy (2005).
Dominant-negative mutant phenotypes and the regulation of translation elongation factor 2 levels in yeast.
  Nucleic Acids Res, 33, 5740-5748.  
16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.
  Nature, 436, 979-984.
PDB codes: 1zm2 1zm3 1zm4 1zm9
16047201 S.Kiparisov, A.Petrov, A.Meskauskas, P.V.Sergiev, O.A.Dontsova, and J.D.Dinman (2005).
Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae.
  Mol Genet Genomics, 274, 235-247.  
15294894 C.L.Hanson, H.Videler, C.Santos, J.P.Ballesta, and C.V.Robinson (2004).
Mass spectrometry of ribosomes from Saccharomyces cerevisiae: implications for assembly of the stalk complex.
  J Biol Chem, 279, 42750-42757.  
15315759 C.M.Spahn, E.Jan, A.Mulder, R.A.Grassucci, P.Sarnow, and J.Frank (2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
  Cell, 118, 465-475.  
15273103 C.Santos, M.A.Rodríguez-Gabriel, M.Remacha, and J.P.Ballesta (2004).
Ribosomal P0 protein domain involved in selectivity of antifungal sordarin derivatives.
  Antimicrob Agents Chemother, 48, 2930-2936.  
15465319 E.V.Orlova, and H.R.Saibil (2004).
Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs.
  Curr Opin Struct Biol, 14, 584-590.  
15334071 J.Sengupta, J.Nilsson, R.Gursky, C.M.Spahn, P.Nissen, and J.Frank (2004).
Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM.
  Nat Struct Mol Biol, 11, 957-962.
PDB code: 1trj
15477390 P.Panopoulos, J.Dresios, and D.Synetos (2004).
Biochemical evidence of translational infidelity and decreased peptidyltransferase activity by a sarcin/ricin domain mutation of yeast 25S rRNA.
  Nucleic Acids Res, 32, 5398-5408.  
15316019 R.Jørgensen, S.P.Yates, D.J.Teal, J.Nilsson, G.A.Prentice, A.R.Merrill, and G.R.Andersen (2004).
Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae.
  J Biol Chem, 279, 45919-45925.
PDB code: 1u2r
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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