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PDBsum entry 1qd7

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protein ligands links
Ribosome PDB id
1qd7
Jmol
Contents
Protein chains
159 a.a.* *
145 a.a.* *
97 a.a.* *
135 a.a.* *
136 a.a.* *
85 a.a.* *
89 a.a.* *
100 a.a.* *
Ligands
__N ×359
* Residue conservation analysis
* C-alpha coords only
PDB id:
1qd7
Name: Ribosome
Title: Partial model for 30s ribosomal subunit
Structure: Central fragment of 16 s RNA. Chain: a. Fragment: residues 563-912. End fragment of 16 s RNA. Chain: b. Fragment: residues 1400-1500. S4 ribosomal protein. Chain: c. S5 ribosomal protein.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Resolution:
5.50Å     R-factor:   not given    
Authors: W.M.Clemons Jr.,J.L.C.May,B.T.Wimberly,J.P.Mccutcheon, M.S.Capel,V.Ramakrishnan
Key ref:
W.M.Clemons et al. (1999). Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature, 400, 833-840. PubMed id: 10476960 DOI: 10.1038/23631
Date:
09-Jul-99     Release date:   31-Aug-99    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P81288  (RS4_GEOSE) -  30S ribosomal protein S4
Seq:
Struc:
200 a.a.
159 a.a.*
Protein chain
Pfam   ArchSchema ?
P02357  (RS5_GEOSE) -  30S ribosomal protein S5
Seq:
Struc:
166 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P23370  (RS6_THETH) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P05766  (RS15_GEOSE) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P23828  (RS17_GEOSE) -  30S ribosomal protein S17
Seq:
Struc:
87 a.a.
89 a.a.*
Protein chain
No UniProt id for this chain
Struc: 100 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/23631 Nature 400:833-840 (1999)
PubMed id: 10476960  
 
 
Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.
W.M.Clemons, J.L.May, B.T.Wimberly, J.P.McCutcheon, M.S.Capel, V.Ramakrishnan.
 
  ABSTRACT  
 
The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Stereo view of the three-way junction formed by helices 20, 21 and 22 of the central domain of 16S RNA. Inset (right) shows the structure in the context of the 30S subunit. Figure made with RIBBONS50.
Figure 5.
Figure 5 Stereo view of the interactions made by helix 27 of the central domain with helices 24 and 44 of 16S RNA. Inset (right) shows the elements in the whole 30S subunit. Figure made with RIBBONS50.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 400, 833-840) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
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
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
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.  
21054500 W.S.Song, S.M.Ryou, H.M.Kim, C.O.Jeon, J.M.Kim, S.H.Han, S.W.Kim, J.P.Szatkiewicz, P.R.Cunningham, and K.Lee (2010).
Functional investigation of residue G791 of Escherichia coli 16S rRNA: implication of initiation factor 1 in the restoration of P-site function.
  FEMS Microbiol Lett, 313, 141-147.  
20127083 Y.Wei, and S.Daunert (2010).
Enabling technologies in discovery: the 2009 Nobel Prize and its implications in antibiotic design.
  Anal Bioanal Chem, 396, 1623-1626.  
19171966 A.M.Karmali, T.L.Blundell, and N.Furnham (2009).
Model-building strategies for low-resolution X-ray crystallographic data.
  Acta Crystallogr D Biol Crystallogr, 65, 121-127.  
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
  Structure, 17, 930-938.  
19325628 D.A.Pomeranz Krummel, C.Oubridge, A.K.Leung, J.Li, and K.Nagai (2009).
Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
  Nature, 458, 475-480.
PDB code: 3cw1
19168615 H.M.Kim, S.M.Ryou, W.S.Song, S.H.Sim, C.J.Cha, S.H.Han, N.C.Ha, J.H.Kim, J.Bae, P.R.Cunningham, and K.Lee (2009).
Genetic analysis of the invariant residue G791 in Escherichia coli 16S rRNA implicates RelA in ribosome function.
  J Bacteriol, 191, 2042-2050.  
19139097 K.Dalal, N.Nguyen, M.Alami, J.Tan, T.F.Moraes, W.C.Lee, R.Maurus, S.S.Sligar, G.D.Brayer, and F.Duong (2009).
Structure, Binding, and Activity of Syd, a SecY-interacting Protein.
  J Biol Chem, 284, 7897-7902.
PDB code: 3ffv
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
19938030 M.Sprinzl, and V.A.Erdmann (2009).
Protein biosynthesis on ribosomes in molecular resolution: nobel prize for chemistry 2009 goes to three chemical biologists.
  Chembiochem, 10, 2851-2853.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
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.  
18468905 J.Heredia-Moya, and K.L.Kirk (2008).
Synthesis of beta-(S-methyl)thioaspartic acid and derivatives.
  Bioorg Med Chem, 16, 5908-5913.  
18824510 M.L.Powell, S.Napthine, R.J.Jackson, I.Brierley, and T.D.Brown (2008).
Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein.
  RNA, 14, 2394-2406.  
18203742 R.Rakauskaite, and J.D.Dinman (2008).
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
  Nucleic Acids Res, 36, 1497-1507.  
17468501 S.Smit, J.Widmann, and R.Knight (2007).
Evolutionary rates vary among rRNA structural elements.
  Nucleic Acids Res, 35, 3339-3354.  
17135184 A.Lescoute, and E.Westhof (2006).
The interaction networks of structured RNAs.
  Nucleic Acids Res, 34, 6587-6604.  
16731530 J.Mengel-Jørgensen, S.S.Jensen, A.Rasmussen, J.Poehlsgaard, J.J.Iversen, and F.Kirpekar (2006).
Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact.
  J Biol Chem, 281, 22108-22117.  
16538608 K.Réblová, F.Lankas, F.Rázga, M.V.Krasovska, J.Koca, and J.Sponer (2006).
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
  Biopolymers, 82, 504-520.  
16407071 L.Yatime, Y.Mechulam, S.Blanquet, and E.Schmitt (2006).
Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer.
  Structure, 14, 119-128.
PDB code: 2aho
15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
  FEBS J, 272, 2098-2108.  
16127068 E.E.Nagiec, L.Wu, S.M.Swaney, J.G.Chosay, D.E.Ross, J.K.Brieland, and K.L.Leach (2005).
Oxazolidinones inhibit cellular proliferation via inhibition of mitochondrial protein synthesis.
  Antimicrob Agents Chemother, 49, 3896-3902.  
15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
  Annu Rev Biochem, 74, 129-177.  
16340009 K.Bhargava, and L.L.Spremulli (2005).
Role of the N- and C-terminal extensions on the activity of mammalian mitochondrial translational initiation factor 3.
  Nucleic Acids Res, 33, 7011-7018.  
16324153 S.Inagaki, K.Numata, T.Kondo, M.Tomita, K.Yasuda, A.Kanai, and Y.Kageyama (2005).
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila.
  Genes Cells, 10, 1163-1173.  
16319080 T.Sakamoto, A.Mahara, K.Yamagata, R.Iwase, T.Yamaoka, and A.Murakami (2005).
Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution.
  Biophys J, 89, 4122-4128.  
15112238 W.P.Tate, and E.S.Poole (2004).
The ribosome: lifting the veil from a fascinating organelle.
  Bioessays, 26, 582-588.  
14573961 D.E.Brodersen, W.M.Clemons, A.P.Carter, B.T.Wimberly, and V.Ramakrishnan (2003).
Phasing the 30S ribosomal subunit structure.
  Acta Crystallogr D Biol Crystallogr, 59, 2044-2050.  
12581310 G.Horiguchi, H.Kodama, and K.Iba (2003).
Mutations in a gene for plastid ribosomal protein S6-like protein reveal a novel developmental process required for the correct organization of lateral root meristem in Arabidopsis.
  Plant J, 33, 521-529.  
14573953 G.Rudenko, L.Henry, C.Vonrhein, G.Bricogne, and J.Deisenhofer (2003).
'MAD'ly phasing the extracellular domain of the LDL receptor: a medium-sized protein, large tungsten clusters and multiple non-isomorphous crystals.
  Acta Crystallogr D Biol Crystallogr, 59, 1978-1986.  
12548625 J.Frank (2003).
Electron microscopy of functional ribosome complexes.
  Biopolymers, 68, 223-233.  
12939790 L.J.Ming (2003).
Structure and function of "metalloantibiotics".
  Med Res Rev, 23, 697-762.  
14527328 P.B.Moore, and T.A.Steitz (2003).
The structural basis of large ribosomal subunit function.
  Annu Rev Biochem, 72, 813-850.  
12620867 S.Behrens, C.Rühland, J.Inácio, H.Huber, A.Fonseca, I.Spencer-Martins, B.M.Fuchs, and R.Amann (2003).
In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.
  Appl Environ Microbiol, 69, 1748-1758.  
12932729 T.A.Steitz, and P.B.Moore (2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
  Trends Biochem Sci, 28, 411-418.  
12490711 J.M.Zimmerman, and L.J.Maher (2002).
In vivo selection of spectinomycin-binding RNAs.
  Nucleic Acids Res, 30, 5425-5435.  
12146982 L.Montoya-García, V.Muñoz-Ocotero, R.Aguilar, and E.Sánchez de Jiménez (2002).
Regulation of acidic ribosomal protein expression and phosphorylation in maize.
  Biochemistry, 41, 10166-10172.  
12209000 M.C.Ganoza, M.C.Kiel, and H.Aoki (2002).
Evolutionary conservation of reactions in translation.
  Microbiol Mol Biol Rev, 66, 460.  
12204683 P.C.Bevilacqua (2002).
Battle for the bulge: directing small molecules to DNA and RNA defects.
  Chem Biol, 9, 854-855.  
12162807 S.Miyata, K.Furuki, K.Oshima, T.Sawayanagi, H.Nishigawa, S.Kakizawa, H.Y.Jung, M.Ugaki, and S.Namba (2002).
Complete nucleotide sequence of the S10-spc operon of phytoplasma: gene organization and genetic code resemble those of Bacillus subtilis.
  DNA Cell Biol, 21, 527-534.  
11341947 A.Walles-Granberg, R.Schnell, L.A.Isaksson, and M.Rydén-Aulin (2001).
Ribosomes with large synthetic N-terminal extensions of protein S15 are active in vivo.
  Biochim Biophys Acta, 1544, 378-385.  
11120937 B.Vester, and S.Douthwaite (2001).
Macrolide resistance conferred by base substitutions in 23S rRNA.
  Antimicrob Agents Chemother, 45, 1.  
11531105 C.M.Niemeyer (2001).
Bioorganic applications of semisynthetic DNA-protein conjugates.
  Chemistry, 7, 3188-3195.  
11389850 C.M.Spahn, G.Blaha, R.K.Agrawal, P.Penczek, R.A.Grassucci, C.A.Trieber, S.R.Connell, D.E.Taylor, K.H.Nierhaus, and J.Frank (2001).
Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.
  Mol Cell, 7, 1037-1045.  
11239155 C.M.Spahn, J.S.Kieft, R.A.Grassucci, P.A.Penczek, K.Zhou, J.A.Doudna, and J.Frank (2001).
Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
  Science, 291, 1959-1962.  
12762005 D.E.Brodersen, A.P.Carter, W.M.Clemons, R.J.Morgan-Warren, F.V.Murphy, J.M.Ogle, M.J.Tarry, B.T.Wimberly, and V.Ramakrishnan (2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
  Cold Spring Harb Symp Quant Biol, 66, 17-32.  
11214183 D.I.Juzumiene, and P.Wollenzien (2001).
Arrangement of the central pseudoknot region of 16S rRNA in the 30S ribosomal subunit determined by site-directed 4-thiouridine crosslinking.
  RNA, 7, 71-84.  
11828423 D.M.Lilley (2001).
The ribosome functions as a ribozyme.
  Chembiochem, 2, 31-35.  
11441810 E.A.Doherty, and J.A.Doudna (2001).
Ribozyme structures and mechanisms.
  Annu Rev Biophys Biomol Struct, 30, 457-475.  
11344316 E.C.Koc, W.Burkhart, K.Blackburn, H.Koc, A.Moseley, and L.L.Spremulli (2001).
Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach.
  Protein Sci, 10, 471-481.  
11566123 G.M.Culver (2001).
Meanderings of the mRNA through the ribosome.
  Structure, 9, 751-758.  
11494321 J.Frank (2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
  Bioessays, 23, 725-732.  
11593008 J.Sengupta, R.K.Agrawal, and J.Frank (2001).
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.
  Proc Natl Acad Sci U S A, 98, 11991-11996.  
11168361 M.C.Kiel, and M.C.Ganoza (2001).
Functional interactions of an Escherichia coli ribosomal ATPase.
  Eur J Biochem, 268, 278-286.  
11258942 P.B.Moore (2001).
The ribosome at atomic resolution.
  Biochemistry, 40, 3243-3250.  
11470155 R.Willumeit, G.Diedrich, S.Forthmann, J.Beckmann, R.P.May, H.B.Stuhrmann, and K.H.Nierhaus (2001).
Mapping proteins of the 50S subunit from Escherichia coli ribosomes.
  Biochim Biophys Acta, 1520, 7.  
11600354 S.K.Wilcox, G.S.Cavey, and J.D.Pearson (2001).
Single ribosomal protein mutations in antibiotic-resistant bacteria analyzed by mass spectrometry.
  Antimicrob Agents Chemother, 45, 3046-3055.  
11327859 T.Yoshida, S.Uchiyama, H.Nakano, H.Kashimori, H.Kijima, T.Ohshima, Y.Saihara, T.Ishino, H.Shimahara, T.Yoshida, K.Yokose, T.Ohkubo, A.Kaji, and Y.Kobayashi (2001).
Solution structure of the ribosome recycling factor from Aquifex aeolicus.
  Biochemistry, 40, 2387-2396.
PDB code: 1ge9
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
11340059 W.Wang, O.Donini, C.M.Reyes, and P.A.Kollman (2001).
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
  Annu Rev Biophys Biomol Struct, 30, 211-243.  
11160931 Y.M.Hou, X.Zhang, J.A.Holland, and D.R.Davis (2001).
An important 2'-OH group for an RNA-protein interaction.
  Nucleic Acids Res, 29, 976-985.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
11121577 A.A.Malygin, D.D.Shaulo, and G.G.Karpova (2000).
Proteins S7, S10, S16 and S19 of the human 40S ribosomal subunit are most resistant to dissociation by salt.
  Biochim Biophys Acta, 1494, 213-216.  
10805779 A.A.Rostom, P.Fucini, D.R.Benjamin, R.Juenemann, K.H.Nierhaus, F.U.Hartl, C.M.Dobson, and C.V.Robinson (2000).
Detection and selective dissociation of intact ribosomes in a mass spectrometer.
  Proc Natl Acad Sci U S A, 97, 5185-5190.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10836789 A.Satoh, K.Takai, R.Ouchi, S.Yokoyama, and H.Takaku (2000).
Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation.
  RNA, 6, 680-686.  
10919826 B.M.Fuchs, F.O.Glöckner, J.Wulf, and R.Amann (2000).
Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes.
  Appl Environ Microbiol, 66, 3603-3607.  
10745014 C.Davies, and S.W.White (2000).
Electrons and X-rays gang up on the ribosome.
  Structure, 8, R41-R45.  
10986461 C.M.Spahn, P.A.Penczek, A.Leith, and J.Frank (2000).
A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
  Structure, 8, 937-948.  
10981630 C.R.Lowe (2000).
Nanobiotechnology: the fabrication and applications of chemical and biological nanostructures.
  Curr Opin Struct Biol, 10, 428-434.  
10799526 D.I.Svergun, and K.H.Nierhaus (2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.
  J Biol Chem, 275, 14432-14439.  
10966470 E.A.Doherty, and J.A.Doudna (2000).
Ribozyme structures and mechanisms.
  Annu Rev Biochem, 69, 597-615.  
10871387 E.Cayama, A.Yépez, F.Rotondo, E.Bandeira, A.C.Ferreras, and F.J.Triana-Alonso (2000).
New chromatographic and biochemical strategies for quick preparative isolation of tRNA.
  Nucleic Acids Res, 28, E64.  
11105763 F.Robert, M.Gagnon, D.Sans, S.Michnick, and L.Brakier-Gingras (2000).
Mapping of the RNA recognition site of Escherichia coli ribosomal protein S7.
  RNA, 6, 1649-1659.  
10998626 G.Evans, P.Roversi, and G.Bricogne (2000).
In-house low-resolution X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 56, 1304-1311.  
10747796 G.W.Muth, S.P.Hennelly, and W.E.Hill (2000).
Using a targeted chemical nuclease to elucidate conformational changes in the E. coli 30S ribosomal subunit.
  Biochemistry, 39, 4068-4074.  
10943895 H.Koosha, D.Cameron, K.Andrews, A.E.Dahlberg, and P.E.March (2000).
Alterations in the peptidyltransferase and decoding domains of ribosomal RNA suppress mutations in the elongation factor G gene.
  RNA, 6, 1166-1173.  
10676812 H.Stark, M.V.Rodnina, H.J.Wieden, M.van Heel, and W.Wintermeyer (2000).
Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation.
  Cell, 100, 301-309.  
10721991 I.S.Gabashvili, R.K.Agrawal, C.M.Spahn, R.A.Grassucci, D.I.Svergun, J.Frank, and P.Penczek (2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
  Cell, 100, 537-549.
PDB code: 1eg0
10943896 I.V.Velichutina, J.Dresios, J.Y.Hong, C.Li, A.Mankin, D.Synetos, and S.W.Liebman (2000).
Mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA affect the function of the decoding center of the ribosome.
  RNA, 6, 1174-1184.  
10889033 J.A.Pleiss, A.D.Wolfson, and O.C.Uhlenbeck (2000).
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.
  Biochemistry, 39, 8250-8258.  
10852723 J.Dresios, I.L.Derkatch, S.W.Liebman, and D.Synetos (2000).
Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable.
  Biochemistry, 39, 7236-7244.  
10968986 J.Sarzynska, T.Kulinski, and L.Nilsson (2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
  Biophys J, 79, 1213-1227.  
10882112 J.Vilardell, S.J.Yu, and J.R.Warner (2000).
Multiple functions of an evolutionarily conserved RNA binding domain.
  Mol Cell, 5, 761-766.  
11000271 J.W.Noah, T.Shapkina, and P.Wollenzien (2000).
UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry.
  Nucleic Acids Res, 28, 3785-3792.  
11095680 J.Wuyts, P.De Rijk, Y.Van de Peer, G.Pison, P.Rousseeuw, and R.De Wachter (2000).
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
  Nucleic Acids Res, 28, 4698-4708.  
11154066 K.R.Katsani, P.Tsiboli, K.Anagnostopoulos, H.Urlaub, and T.Choli-Papadopoulou (2000).
Identification of the 50S ribosomal proteins from the Eubacterium Thermus thermophilus.
  Biol Chem, 381, 1079-1087.  
10836793 L.Lancaster, G.M.Culver, G.Z.Yusupova, J.H.Cate, M.M.Yusupov, and H.F.Noller (2000).
The location of protein S8 and surrounding elements of 16S rRNA in the 70S ribosome from combined use of directed hydroxyl radical probing and X-ray crystallography.
  RNA, 6, 717-729.
PDB code: 1emi
10637222 M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, and R.Huber (2000).
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
  EMBO J, 19, 174-186.
PDB codes: 1dd3 1dd4
10835368 M.G.Gomez-Lorenzo, C.M.Spahn, R.K.Agrawal, R.A.Grassucci, P.Penczek, K.Chakraburtty, J.P.Ballesta, J.L.Lavandera, J.F.Garcia-Bustos, and J.Frank (2000).
Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution.
  EMBO J, 19, 2710-2718.  
10696113 M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  Proc Natl Acad Sci U S A, 97, 2023-2028.
PDB code: 1dfu
10592212 M.Szymanski, M.Z.Barciszewska, J.Barciszewski, and V.A.Erdmann (2000).
5S ribosomal RNA database Y2K.
  Nucleic Acids Res, 28, 166-167.  
10698923 M.Worbs, R.Huber, and M.C.Wahl (2000).
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
  EMBO J, 19, 807-818.
PDB code: 1dmg
10937989 N.Ban, P.Nissen, J.Hansen, P.B.Moore, and T.A.Steitz (2000).
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
  Science, 289, 905-920.
PDB code: 1ffk
11142373 N.Demeshkina, M.Repkova, A.Ven'yaminova, D.Graifer, and G.Karpova (2000).
Nucleotides of 18S rRNA surrounding mRNA codons at the human ribosomal A, P, and E sites: a crosslinking study with mRNA analogs carrying an aryl azide group at either the uracil or the guanine residue.
  RNA, 6, 1727-1736.  
10801481 N.Nevskaya, S.Tischenko, R.Fedorov, S.Al-Karadaghi, A.Liljas, A.Kraft, W.Piendl, M.Garber, and S.Nikonov (2000).
Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family.
  Structure, 8, 363-371.
PDB code: 1cjs
10949037 N.Polacek, S.Patzke, K.H.Nierhaus, and A.Barta (2000).
Periodic conformational changes in rRNA: monitoring the dynamics of translating ribosomes.
  Mol Cell, 6, 159-171.  
11004163 N.S.Chernyaeva, and E.J.Murgola (2000).
Covariance of complementary rRNA loop nucleotides does not necessarily represent functional pseudoknot formation in vivo.
  J Bacteriol, 182, 5671-5675.  
10997906 P.Allard, A.V.Rak, B.T.Wimberly, W.M.Clemons, A.Kalinin, M.Helgstrand, M.B.Garber, V.Ramakrishnan, and T.Härd (2000).
Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit.
  Structure, 8, 875-882.
PDB code: 1emw
10675317 P.Nissen, M.Kjeldgaard, and J.Nyborg (2000).
Macromolecular mimicry.
  EMBO J, 19, 489-495.  
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
10837219 R.Green (2000).
Ribosomal translocation: EF-G turns the crank.
  Curr Biol, 10, R369-R373.  
10931859 R.K.Agrawal, C.M.Spahn, P.Penczek, R.A.Grassucci, K.H.Nierhaus, and J.Frank (2000).
Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle.
  J Cell Biol, 150, 447-460.
PDB code: 1fcw
10619838 R.Schroeder, C.Waldsich, and H.Wank (2000).
Modulation of RNA function by aminoglycoside antibiotics.
  EMBO J, 19, 1-9.
PDB codes: 1qhn 1qhs 1qhx 1qhy
10679458 S.Blanquet, Y.Mechulam, and E.Schmitt (2000).
The many routes of bacterial transfer RNAs after aminoacylation.
  Curr Opin Struct Biol, 10, 95.  
10753109 S.C.Agalarov, G.Sridhar Prasad, P.M.Funke, C.D.Stout, and J.R.Williamson (2000).
Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain.
  Science, 288, 107-113.
PDB codes: 1ekc 1g1x
10744024 S.C.Agalarov, and J.R.Williamson (2000).
A hierarchy of RNA subdomains in assembly of the central domain of the 30 S ribosomal subunit.
  RNA, 6, 402-408.  
11114498 S.Chandra Sanyal, and A.Liljas (2000).
The end of the beginning: structural studies of ribosomal proteins.
  Curr Opin Struct Biol, 10, 633-636.  
10781065 U.Stelzl, C.M.Spahn, and K.H.Nierhaus (2000).
Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: application of a method called SERF.
  Proc Natl Acad Sci U S A, 97, 4597-4602.  
10787170 V.I.Zannis, and J.Cohen (2000).
Old and new players in the lipoprotein system.
  Curr Opin Lipidol, 11, 101-103.  
11050428 W.C.Lathe, B.Snel, and P.Bork (2000).
Gene context conservation of a higher order than operons.
  Trends Biochem Sci, 25, 474-479.  
10969026 W.Wriggers, R.K.Agrawal, D.L.Drew, A.McCammon, and J.Frank (2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
  Biophys J, 79, 1670-1678.  
10588692 A.Tocilj, F.Schlünzen, D.Janell, M.Glühmann, H.A.Hansen, J.Harms, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, and A.Yonath (1999).
The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.
  Proc Natl Acad Sci U S A, 96, 14252-14257.
PDB codes: 1c59 1dv4
10579710 A.Verschoor, and T.Lithgow (1999).
A first glimpse at the structure of the TOM translocase from the mitochondrial outer membrane.
  J Cell Biol, 147, 905-908.  
10647187 C.M.Spahn, R.A.Grassucci, P.Penczek, and J.Frank (1999).
Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy.
  Structure, 7, 1567-1573.  
10562562 I.S.Gabashvili, R.K.Agrawal, R.Grassucci, C.L.Squires, A.E.Dahlberg, and J.Frank (1999).
Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA.
  EMBO J, 18, 6501-6507.  
10530999 J.A.Doudna (1999).
Cashing in on crystals.
  Curr Biol, 9, R731-R734.  
10497122 J.H.Cate, M.M.Yusupov, G.Z.Yusupova, T.N.Earnest, and H.F.Noller (1999).
X-ray crystal structures of 70S ribosome functional complexes.
  Science, 285, 2095-2104.
PDB code: 486d
10583945 M.Ibba, and D.Söll (1999).
Quality control mechanisms during translation.
  Science, 286, 1893-1897.  
10647188 R.Matadeen, A.Patwardhan, B.Gowen, E.V.Orlova, T.Pape, M.Cuff, F.Mueller, R.Brimacombe, and M.van Heel (1999).
The Escherichia coli large ribosomal subunit at 7.5 A resolution.
  Structure, 7, 1575-1583.  
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.