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PDBsum entry 1k5y
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protein dna_rna links
Ribosome PDB id
1k5y
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.*
78 a.a.*
109 a.a.*
59 a.a.*
52 a.a.*
91 a.a.*
73 a.a.*
DNA/RNA
* C-alpha coords only
Theoretical model
PDB id:
1k5y
Name: Ribosome
Title: Structure of the translating 80s ribosome from yeast, obtained by docking atomic models for RNA and protein components into a 15a cryo-em map. This file 1k5y contains the 60s ribosomal subunit. The file 1k5x contains the 40s ribosomal subunit, the p-site bound tRNA and the mRNA codon.
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 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. Yeast. Yeast
Authors: C.M.T.Spahn,R.Beckmann,N.Eswar,P.Penczek,A.Sali,G.Blobel, J.Frank
Key ref:
C.M.Spahn et al. (2001). Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell, 107, 373-386. PubMed id: 11701127 DOI: 10.1016/S0092-8674(01)00539-6
Date:
12-Oct-01     Release date:   09-Nov-01    
 Headers
 References

Protein chain
P53030  (RL1_YEAST) - 
Protein chain
P05736  (RL2_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P14126  (RL3_YEAST) -  60S ribosomal protein L3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		387 a.a.
359 a.a.
Protein chain
Pfam   ArchSchema ?
P10664  (RL4A_YEAST) -  60S ribosomal protein L4-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		362 a.a.
256 a.a.
Protein chain
Pfam   ArchSchema ?
P26321  (RL5_YEAST) -  60S ribosomal protein L5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		297 a.a.
222 a.a.*
Protein chain
Pfam   ArchSchema ?
P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		244 a.a.
161 a.a.
Protein chain
Pfam   ArchSchema ?
P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		256 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		191 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P41805  (RL10_YEAST) -  60S ribosomal protein L10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		221 a.a.
165 a.a.
Protein chain
P06380  (RL11_YEAST) - 
Protein chain
P17079  (RL12_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		204 a.a.
194 a.a.
Protein chain
Pfam   ArchSchema ?
P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		199 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		184 a.a.
147 a.a.
Protein chain
P07279  (RL18_YEAST) - 
Protein chain
P05735  (RL19_YEAST) - 
Protein chain
Pfam   ArchSchema ?
Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		160 a.a.
97 a.a.
Protein chain
P04451  (RL23_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P04456  (RL25_YEAST) -  60S ribosomal protein L25 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		142 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		127 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P02406  (RL28_YEAST) -  60S ribosomal protein L28 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		149 a.a.
143 a.a.*
Protein chain
P04649  (RL31_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P38061  (RL32_YEAST) -  60S ribosomal protein L32 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		130 a.a.
109 a.a.
Protein chain
P39741  (RL35_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		88 a.a.
52 a.a.
Protein chain
P02405  (RL44_YEAST) - 
Protein chain
P49631  (RL43_YEAST) - 
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains
  A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A-A- ... 2816 bases
  U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U-C- 121 bases

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(01)00539-6 Cell 107:373-386 (2001)
PubMed id: 11701127  
 
 
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, J.Frank.
 
  ABSTRACT  
 
A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. rRNA Secondary Structure DiagramsSecondary structure diagrams of the 18S rRNA (a) and the 5.8/25S rRNA (b) of S. cerevisiae (http://www.rna.icmb.utexas.edu). Expansion segments in the rRNAs are indicated, using the nomenclature of Gerbi (1996) 		Figure 6.
Figure 6. Position of the Intersubunit BridgesThe 40S subunit in yellow (a) and the 60S subunit in blue (b) are shown from their intersubunit sides. The intersubunit bridges are shown in red and are annotated with their numbers. Bridges also observed in prokaryotic ribosomes are numbered B1–B7. Additional intersubunit connections in the yeast ribosome are named eB8–eB11 (see also Table 1)
 
  The above figures are reprinted by permission from Cell Press: Cell (2001, 107, 373-386) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142978 B.Bradatsch, C.Leidig, S.Granneman, M.Gnädig, D.Tollervey, B.Böttcher, R.Beckmann, and E.Hurt (2012).
Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.
  Nat Struct Mol Biol, 19, 1234-1241.
PDB code: 3j2i
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21283762 M.G.Campbell, and K.Karbstein (2011).
Protein-Protein Interactions within Late Pre-40S Ribosomes.
  PLoS One, 6, e16194.  
21343906 M.Schepetilnikov, K.Kobayashi, A.Geldreich, C.Caranta, C.Robaglia, M.Keller, and L.A.Ryabova (2011).
Viral factor TAV recruits TOR/S6K1 signalling to activate reinitiation after long ORF translation.
  EMBO J, 30, 1343-1356.  
21076851 N.Malys, and J.E.McCarthy (2011).
Translation initiation: variations in the mechanism can be anticipated.
  Cell Mol Life Sci, 68, 991.  
21138965 Q.Sun, A.Vila-Sanjurjo, and M.O'Connor (2011).
Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit-subunit interactions on the 70S ribosome.
  Nucleic Acids Res, 39, 3321-3330.  
21400046 Q.Xie, J.Lin, Y.Qin, J.Zhou, and W.Bu (2011).
Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
  Protein Cell, 2, 161-170.  
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
20008552 E.Thomson, and D.Tollervey (2010).
The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae.
  Mol Cell Biol, 30, 976-984.  
20799971 F.Zhou, B.Roy, and A.G.von Arnim (2010).
Translation reinitiation and development are compromised in similar ways by mutations in translation initiation factor eIF3h and the ribosomal protein RPL24.
  BMC Plant Biol, 10, 193.  
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
20980660 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).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB codes: 3izb 3izc 3izd 3ize 3izf 3izs
20584915 J.Sengupta, C.Bussiere, J.Pallesen, M.West, A.W.Johnson, and J.Frank (2010).
Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit.
  J Cell Biol, 189, 1079-1086.  
20434207 J.Tcherkezian, P.A.Brittis, F.Thomas, P.P.Roux, and J.G.Flanagan (2010).
Transmembrane receptor DCC associates with protein synthesis machinery and regulates translation.
  Cell, 141, 632-644.  
20876129 K.Kobayashi, I.Kikuno, K.Kuroha, K.Saito, K.Ito, R.Ishitani, T.Inada, and O.Nureki (2010).
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.
  Proc Natl Acad Sci U S A, 107, 17575-17579.
PDB codes: 3agj 3wxm
20060839 L.Elantak, S.Wagner, A.Herrmannová, M.Karásková, E.Rutkai, P.J.Lukavsky, and L.Valásek (2010).
The indispensable N-terminal half of eIF3j/HCR1 cooperates with its structurally conserved binding partner eIF3b/PRT1-RRM and with eIF1A in stringent AUG selection.
  J Mol Biol, 396, 1097-1116.  
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.  
  20836845 M.J.Raupach, J.J.Astrin, K.Hannig, M.K.Peters, M.Y.Stoeckle, and J.W.Wägele (2010).
Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes.
  Front Zool, 7, 26.  
20584913 M.Oeffinger (2010).
Joining the interface: a site for Nmd3 association on 60S ribosome subunits.
  J Cell Biol, 189, 1071-1073.  
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.  
20392820 R.Babiano, and J.de la Cruz (2010).
Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae.
  Nucleic Acids Res, 38, 5177-5192.  
20094052 R.J.Jackson, C.U.Hellen, and T.V.Pestova (2010).
The mechanism of eukaryotic translation initiation and principles of its regulation.
  Nat Rev Mol Cell Biol, 11, 113-127.  
20453830 S.Granneman, E.Petfalski, A.Swiatkowska, and D.Tollervey (2010).
Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking.
  EMBO J, 29, 2026-2036.  
20534490 S.Kurata, K.H.Nielsen, S.F.Mitchell, J.R.Lorsch, A.Kaji, and H.Kaji (2010).
Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.
  Proc Natl Acad Sci U S A, 107, 10854-10859.  
19969550 T.Lumsden, A.A.Bentley, W.Beutler, A.Ghosh, O.Galkin, and A.A.Komar (2010).
Yeast strains with N-terminally truncated ribosomal protein S5: implications for the evolution, structure and function of the Rps5/Rps7 proteins.
  Nucleic Acids Res, 38, 1261-1272.  
20584985 W.L.Chiu, S.Wagner, A.Herrmannová, L.Burela, F.Zhang, A.K.Saini, L.Valásek, and A.G.Hinnebusch (2010).
The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons.
  Mol Cell Biol, 30, 4415-4434.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  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.  
19820108 A.Baudin-Baillieu, C.Fabret, X.H.Liang, D.Piekna-Przybylska, M.J.Fournier, and J.P.Rousset (2009).
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy.
  Nucleic Acids Res, 37, 7665-7677.  
19801658 B.Pertschy, C.Schneider, M.Gnädig, T.Schäfer, D.Tollervey, and E.Hurt (2009).
RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1.
  J Biol Chem, 284, 35079-35091.  
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.  
19850913 B.S.Strunk, and K.Karbstein (2009).
Powering through ribosome assembly.
  RNA, 15, 2083-2104.  
19287397 C.S.Fraser, J.W.Hershey, and J.A.Doudna (2009).
The pathway of hepatitis C virus mRNA recruitment to the human ribosome.
  Nat Struct Mol Biol, 16, 397-404.  
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.  
19737519 C.Ulbrich, M.Diepholz, J.Bassler, D.Kressler, B.Pertschy, K.Galani, B.Böttcher, and E.Hurt (2009).
Mechanochemical removal of ribosome biogenesis factors from nascent 60S ribosomal subunits.
  Cell, 138, 911-922.  
19861425 D.Hasenöhrl, A.Fabbretti, P.Londei, C.O.Gualerzi, and U.Bläsi (2009).
Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus.
  RNA, 15, 2288-2298.  
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
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19897894 H.J.Ha, W.S.Song, H.M.Kim, H.S.Son, and K.Lee (2009).
Functional study of the residue C899 in the 900 tetraloop of Escherichia coli small subunit ribosomal RNA.
  Biosci Biotechnol Biochem, 73, 2544-2546.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
19625386 M.H.Mazauric, J.L.Leroy, K.Visscher, S.Yoshizawa, and D.Fourmy (2009).
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
  RNA, 15, 1775-1786.  
19497863 M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, and R.K.Agrawal (2009).
Structure of a mitochondrial ribosome with minimal RNA.
  Proc Natl Acad Sci U S A, 106, 9637-9642.
PDB codes: 3iy8 3iy9
19745810 O.Thiébeauld, M.Schepetilnikov, H.S.Park, A.Geldreich, K.Kobayashi, M.Keller, T.Hohn, and L.A.Ryabova (2009).
A new plant protein interacts with eIF3 and 60S to enhance virus-activated translation re-initiation.
  EMBO J, 28, 3171-3184.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19191325 R.Cmejla, J.Cmejlova, H.Handrkova, J.Petrak, K.Petrtylova, V.Mihal, J.Stary, Z.Cerna, Y.Jabali, and D.Pospisilova (2009).
Identification of mutations in the ribosomal protein L5 (RPL5) and ribosomal protein L11 (RPL11) genes in Czech patients with Diamond-Blackfan anemia.
  Hum Mutat, 30, 321-327.  
19419242 R.E.Halbeisen, and A.P.Gerber (2009).
Stress-Dependent Coordination of Transcriptome and Translatome in Yeast.
  PLoS Biol, 7, e105.  
19432457 S.P.Edmondson, J.Turri, K.Smith, A.Clark, and J.W.Shriver (2009).
Structure, stability, and flexibility of ribosomal protein L14e from Sulfolobus solfataricus.
  Biochemistry, 48, 5553-5562.  
18208838 A.B.Taylor, B.Meyer, B.Z.Leal, P.Kötter, V.Schirf, B.Demeler, P.J.Hart, K.D.Entian, and J.Wöhnert (2008).
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
  Nucleic Acids Res, 36, 1542-1554.
PDB codes: 3bbd 3bbe 3bbh
18369869 A.Görg, C.Lück, and W.Weiss (2008).
Sample prefractionation in granulated sephadex IEF gels.
  Methods Mol Biol, 424, 277-286.  
18263608 A.Meskauskas, J.R.Russ, and J.D.Dinman (2008).
Structure/function analysis of yeast ribosomal protein L2.
  Nucleic Acids Res, 36, 1826-1835.  
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.  
18820293 A.Perreault, C.Bellemer, and F.Bachand (2008).
Nuclear export competence of pre-40S subunits in fission yeast requires the ribosomal protein Rps2.
  Nucleic Acids Res, 36, 6132-6142.  
18464793 A.V.Pisarev, V.G.Kolupaeva, M.M.Yusupov, C.U.Hellen, and T.V.Pestova (2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
  EMBO J, 27, 1609-1621.  
18765792 B.Szamecz, E.Rutkai, L.Cuchalová, V.Munzarová, A.Herrmannová, K.H.Nielsen, L.Burela, A.G.Hinnebusch, and L.Valásek (2008).
eIF3a cooperates with sequences 5' of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA.
  Genes Dev, 22, 2414-2425.  
18218711 B.Wu, A.Yee, Y.J.Huang, T.A.Ramelot, J.R.Cort, A.Semesi, J.W.Jung, W.Lee, G.T.Montelione, M.A.Kennedy, and C.H.Arrowsmith (2008).
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain.
  Protein Sci, 17, 583-588.
PDB code: 1rq6
18157151 D.A.Costantino, J.S.Pfingsten, R.P.Rambo, and J.S.Kieft (2008).
tRNA-mRNA mimicry drives translation initiation from a viral IRES.
  Nat Struct Mol Biol, 15, 57-64.
PDB code: 3b31
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.  
18560357 H.F.Horn, and K.H.Vousden (2008).
Cooperation between the ribosomal proteins L5 and L11 in the p53 pathway.
  Oncogene, 27, 5774-5784.  
18438419 H.W.Gabel, and G.Ruvkun (2008).
The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi.
  Nat Struct Mol Biol, 15, 531-533.  
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).
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18535205 J.E.Farrar, M.Nater, E.Caywood, M.A.McDevitt, J.Kowalski, C.M.Takemoto, C.C.Talbot, P.Meltzer, D.Esposito, A.H.Beggs, H.E.Schneider, A.Grabowska, S.E.Ball, E.Niewiadomska, C.A.Sieff, A.Vlachos, E.Atsidaftos, S.R.Ellis, J.M.Lipton, H.T.Gazda, and R.J.Arceci (2008).
Abnormalities of the large ribosomal subunit protein, Rpl35a, in Diamond-Blackfan anemia.
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18515544 J.S.Pfingsten, and J.S.Kieft (2008).
RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.
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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.
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PDB codes: 3dny 3dwu
18637734 K.Bakowska-Zywicka, A.M.Kietrys, and T.Twardowski (2008).
Antisense oligonucleotides targeting universally conserved 26S rRNA domains of plant ribosomes at different steps of polypeptide elongation.
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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.
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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.
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PDB codes: 2zkq 2zkr
18344525 P.Y.Liao, P.Gupta, A.N.Petrov, J.D.Dinman, and K.H.Lee (2008).
A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting.
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18566829 R.F.Degenhardt, and P.C.Bonham-Smith (2008).
Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog.
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18456707 T.Yokoyama, and T.Suzuki (2008).
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19088750 Y.S.Khairulina, M.V.Molotkov, K.N.Bulygin, D.M.Graifer, A.G.Ven'yaminova, L.Y.Frolova, J.Stahl, and G.G.Karpova (2008).
[Protein S3 Fragments Neighboring mRNA during Elongation and Translation Termination on the Human Ribosome.]
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17599068 A.Catic, Z.Y.Sun, D.M.Ratner, S.Misaghi, E.Spooner, J.Samuelson, G.Wagner, and H.L.Ploegh (2007).
Sequence and structure evolved separately in a ribosomal ubiquitin variant.
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PDB code: 2jx5
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.
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17761675 A.Hofer, C.Bussiere, and A.W.Johnson (2007).
Mutational analysis of the ribosomal protein Rpl10 from yeast.
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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.
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17956730 A.V.Pisarev, C.U.Hellen, and T.V.Pestova (2007).
Recycling of eukaryotic posttermination ribosomal complexes.
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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.
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17128284 C.S.Fraser, and J.A.Doudna (2007).
Structural and mechanistic insights into hepatitis C viral translation initiation.
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18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
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Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
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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.
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17329356 D.Taliaferro, and P.J.Farabaugh (2007).
An mRNA sequence derived from the yeast EST3 gene stimulates programmed +1 translational frameshifting.
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17710148 G.P.Henderson, L.Gan, and G.J.Jensen (2007).
3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell.
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18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
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Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments.
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17938242 J.Zhang, P.Harnpicharnchai, J.Jakovljevic, L.Tang, Y.Guo, M.Oeffinger, M.P.Rout, S.L.Hiley, T.Hughes, and J.L.Woolford (2007).
Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes.
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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.
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17711575 L.Pnueli, and Y.Arava (2007).
Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9.
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17521915 M.J.Suh, S.Pourshahian, and P.A.Limbach (2007).
Developing limited proteolysis and mass spectrometry for the characterization of ribosome topography.
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17564727 M.O'connor (2007).
Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli.
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17886434 M.V.Molotkov, D.M.GraÄ­fer, E.A.Popugaeva, K.N.Bulygin, M.I.Meshchaninova, A.G.Ven'iaminova, and G.G.Karpova (2007).
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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.
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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.
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17548477 P.Martín-Marcos, A.G.Hinnebusch, and M.Tamame (2007).
Ribosomal protein L33 is required for ribosome biogenesis, subunit joining, and repression of GCN4 translation.
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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.
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17921318 S.Chaudhuri, K.Vyas, P.Kapasi, A.A.Komar, J.D.Dinman, S.Barik, and B.Mazumder (2007).
Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation.
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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.
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17889647 S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, and B.P.Klaholz (2007).
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
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PDB code: 2vaz
17545469 S.Röther, and K.Strässer (2007).
The RNA polymerase II CTD kinase Ctk1 functions in translation elongation.
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17468501 S.Smit, J.Widmann, and R.Knight (2007).
Evolutionary rates vary among rRNA structural elements.
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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.
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17434126 W.Yao, D.Roser, A.Köhler, B.Bradatsch, J.Bassler, and E.Hurt (2007).
Nuclear export of ribosomal 60S subunits by the general mRNA export receptor Mex67-Mtr2.
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16920360 A.G.Hinnebusch (2006).
eIF3: a versatile scaffold for translation initiation complexes.
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16891309 A.Liiv, and M.O'Connor (2006).
Mutations in the intersubunit bridge regions of 23 S rRNA.
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16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
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16721598 A.W.Strittmatter, C.Fischer, M.Kleinschmidt, and G.H.Braus (2006).
FLO11 mediated filamentous growth of the yeast Saccharomyces cerevisiae depends on the expression of the ribosomal RPS26 genes.
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16437570 B.K.Rai, and A.Fiser (2006).
Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
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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.
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PDB codes: 2iw3 2iwh 2ix3 2ix8
17381300 D.C.Zappulla, and T.R.Cech (2006).
RNA as a flexible scaffold for proteins: yeast telomerase and beyond.
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16581790 D.E.Andreev, I.M.Terenin, Y.E.Dunaevsky, S.E.Dmitriev, and I.N.Shatsky (2006).
A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors.
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16307820 E.Jan (2006).
Divergent IRES elements in invertebrates.
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16614452 E.Laletina, D.Graifer, A.Malygin, A.Ivanov, I.Shatsky, and G.Karpova (2006).
Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit.
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16808174 E.S.Laletina, D.M.GraÄ­fer, A.A.Malygin, I.N.ShatskiÄ­, and G.G.Karpova (2006).
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16362046 I.B.Lomakin, N.E.Shirokikh, M.M.Yusupov, C.U.Hellen, and T.V.Pestova (2006).
The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH.
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16713251 J.Bravo, and P.Aloy (2006).
Target selection for complex structural genomics.
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16553873 J.Dresios, P.Panopoulos, and D.Synetos (2006).
Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function.
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An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes.
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17069639 J.J.Gillespie, J.S.Johnston, J.J.Cannone, and R.R.Gutell (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
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16890441 K.P.Hofmann, C.M.Spahn, R.Heinrich, and U.Heinemann (2006).
Building functional modules from molecular interactions.
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16565414 L.D.Kapp, S.E.Kolitz, and J.R.Lorsch (2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.
  RNA, 12, 751-764.  
16721597 M.Buchhaupt, B.Meyer, P.Kötter, and K.D.Entian (2006).
Genetic evidence for 18S rRNA binding and an Rps19p assembly function of yeast nucleolar protein Nep1p.
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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
17012271 N.E.McCrate, M.E.Varner, K.I.Kim, and M.C.Nagan (2006).
Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.
  Nucleic Acids Res, 34, 5361-5368.  
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.
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16888326 R.M.Seiser, A.E.Sundberg, B.J.Wollam, P.Zobel-Thropp, K.Baldwin, M.D.Spector, and D.E.Lycan (2006).
Ltv1 is required for efficient nuclear export of the ribosomal small subunit in Saccharomyces cerevisiae.
  Genetics, 174, 679-691.  
16940977 S.M.Klauck, B.Felder, A.Kolb-Kokocinski, C.Schuster, A.Chiocchetti, I.Schupp, R.Wellenreuther, G.Schmötzer, F.Poustka, L.Breitenbach-Koller, and A.Poustka (2006).
Mutations in the ribosomal protein gene RPL10 suggest a novel modulating disease mechanism for autism.
  Mol Psychiatry, 11, 1073-1084.  
16715044 S.P.Ryder (2006).
Oskar gains weight.
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16950778 T.Komoda, N.S.Sato, S.S.Phelps, N.Namba, S.Joseph, and T.Suzuki (2006).
The A-site finger in 23 S rRNA acts as a functional attenuator for translocation.
  J Biol Chem, 281, 32303-32309.  
16738661 T.Schäfer, B.Maco, E.Petfalski, D.Tollervey, B.Böttcher, U.Aebi, and E.Hurt (2006).
Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.
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15654870 A.D.van Dijk, R.Boelens, and A.M.Bonvin (2005).
Data-driven docking for the study of biomolecular complexes.
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16314511 A.Meskauskas, A.N.Petrov, and J.D.Dinman (2005).
Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis.
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16322461 B.Siridechadilok, C.S.Fraser, R.J.Hall, J.A.Doudna, and E.Nogales (2005).
Structural roles for human translation factor eIF3 in initiation of protein synthesis.
  Science, 310, 1513-1515.  
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.
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16271893 D.Boehringer, R.Thermann, A.Ostareck-Lederer, J.D.Lewis, and H.Stark (2005).
Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.
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PDB code: 2agn
16081657 D.Korkin, F.P.Davis, and A.Sali (2005).
Localization of protein-binding sites within families of proteins.
  Protein Sci, 14, 2350-2360.  
16257826 D.N.Wilson, and K.H.Nierhaus (2005).
Ribosomal proteins in the spotlight.
  Crit Rev Biochem Mol Biol, 40, 243-267.  
  18074004 J.D.Dinman (2005).
5S rRNA: Structure and Function from Head to Toe.
  Int J Biomed Sci, 1, 2-7.  
16244664 J.Dudek, M.Greiner, A.Müller, L.M.Hendershot, K.Kopsch, W.Nastainczyk, and R.Zimmermann (2005).
ERj1p has a basic role in protein biogenesis at the endoplasmic reticulum.
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16271881 J.H.Cate (2005).
The ins and outs of protein synthesis.
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15660131 J.Hedges, M.West, and A.W.Johnson (2005).
Release of the export adapter, Nmd3p, from the 60S ribosomal subunit requires Rpl10p and the cytoplasmic GTPase Lsg1p.
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16313563 J.J.Gillespie, C.H.McKenna, M.J.Yoder, R.R.Gutell, J.S.Johnston, J.Kathirithamby, and A.I.Cognato (2005).
Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).
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Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes.
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15629717 M.Bekaert, and J.P.Rousset (2005).
An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA.
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16244660 M.Blau, S.Mullapudi, T.Becker, J.Dudek, R.Zimmermann, P.A.Penczek, and R.Beckmann (2005).
ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.
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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
16120833 M.Sumita, J.P.Desaulniers, Y.C.Chang, H.M.Chui, L.Clos, and C.S.Chow (2005).
Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA.
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15831484 M.West, J.B.Hedges, A.Chen, and A.W.Johnson (2005).
Defining the order in which Nmd3p and Rpl10p load onto nascent 60S ribosomal subunits.
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16287850 S.Granneman, M.R.Nandineni, and S.J.Baserga (2005).
The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.
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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.
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15703437 V.G.Kolupaeva, A.Unbehaun, I.B.Lomakin, C.U.Hellen, and T.V.Pestova (2005).
Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association.
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16254050 Y.Yamamoto, C.R.Singh, A.Marintchev, N.S.Hall, E.M.Hannig, G.Wagner, and K.Asano (2005).
The eukaryotic initiation factor (eIF) 5 HEAT domain mediates multifactor assembly and scanning with distinct interfaces to eIF1, eIF2, eIF3, and eIF4G.
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15352330 A.Habura, D.R.Rosen, and S.S.Bowser (2004).
Predicted secondary structure of the foraminiferal SSU 3' major domain reveals a molecular synapomorphy for granuloreticulosean protists.
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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.
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14976550 C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, and J.Frank (2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
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PDB codes: 1s1h 1s1i
15078877 C.Shirai, T.Takai, M.Nariai, C.Horigome, and K.Mizuta (2004).
Ebp2p, the yeast homolog of Epstein-Barr virus nuclear antigen 1-binding protein 2, interacts with factors of both the 60 S and the 40 s ribosomal subunit assembly.
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15093836 C.Vogel, M.Bashton, N.D.Kerrison, C.Chothia, and S.A.Teichmann (2004).
Structure, function and evolution of multidomain proteins.
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15208366 D.Graifer, M.Molotkov, V.Styazhkina, N.Demeshkina, K.Bulygin, A.Eremina, A.Ivanov, E.Laletina, A.Ven'yaminova, and G.Karpova (2004).
Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites.
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15289434 E.R.Oliver, T.L.Saunders, S.A.Tarlé, and T.Glaser (2004).
Ribosomal protein L24 defect in belly spot and tail (Bst), a mouse Minute.
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14872060 E.Saijou, T.Fujiwara, T.Suzaki, K.Inoue, and H.Sakamoto (2004).
RBD-1, a nucleolar RNA-binding protein, is essential for Caenorhabditis elegans early development through 18S ribosomal RNA processing.
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15175657 F.Bachand, and P.A.Silver (2004).
PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits.
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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.
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PDB code: 1trj
15611164 J.W.Loar, R.M.Seiser, A.E.Sundberg, H.J.Sagerson, N.Ilias, P.Zobel-Thropp, E.A.Craig, and D.E.Lycan (2004).
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The molecular mechanics of eukaryotic translation.
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Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
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PDB code: 1ry1
15383681 M.T.Howard, R.F.Gesteland, and J.F.Atkins (2004).
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15193311 R.B.Russell, F.Alber, P.Aloy, F.P.Davis, D.Korkin, M.Pichaud, M.Topf, and A.Sali (2004).
A structural perspective on protein-protein interactions.
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15068803 R.J.Gilbert, P.Fucini, S.Connell, S.D.Fuller, K.H.Nierhaus, C.V.Robinson, C.M.Dobson, and D.I.Stuart (2004).
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15037769 U.Maiväli, and J.Remme (2004).
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From words to literature in structural proteomics.
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Ribosomal proteins Rps0 and Rps21 of Saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18S rRNA.
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Comparative protein structure modeling by iterative alignment, model building and model assessment.
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The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
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Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
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PDB codes: 1p6g 1p85 1p86 1p87
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12960421 J.C.Politz, R.A.Tuft, and T.Pederson (2003).
Diffusion-based transport of nascent ribosomes in the nucleus.
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The yeast eIF3 subunits TIF32/a, NIP1/c, and eIF5 make critical connections with the 40S ribosome in vivo.
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Understanding and Predicting Protein Assemblies With 3D Structures.
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Rpf2p, an evolutionarily conserved protein, interacts with ribosomal protein L11 and is essential for the processing of 27 SB Pre-rRNA to 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae.
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Comparative analysis of multiple genome-scale data sets.
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Rlp7p is associated with 60S preribosomes, restricted to the granular component of the nucleolus, and required for pre-rRNA processing.
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Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.
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The third dimension for protein interactions and complexes.
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MODBASE, a database of annotated comparative protein structure models.
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The active 80S ribosome-Sec61 complex.
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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 code is shown on the right.

 

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