spacer
spacer

PDBsum entry 1i97

Go to PDB code: 
protein dna_rna ligands metals links
Ribosome PDB id
1i97
Jmol
Contents
Protein chains
249 a.a.* *
206 a.a.* *
208 a.a.* *
156 a.a.* *
101 a.a.* *
155 a.a.* *
138 a.a.* *
127 a.a.* *
98 a.a.* *
123 a.a.* *
131 a.a.* *
93 a.a.* *
60 a.a.* *
88 a.a.* *
88 a.a.* *
104 a.a.* *
82 a.a.* *
80 a.a.* *
99 a.a.* *
24 a.a.* *
DNA/RNA
Ligands
WO2 ×14
TAC ×6
Metals
_MG ×75
_ZN ×2
* Residue conservation analysis
* C-alpha coords only
PDB id:
1i97
Name: Ribosome
Title: Crystal structure of the 30s ribosomal subunit from thermus thermophilus in complex with tetracycline
Structure: 16s rrna. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: 21mer (from PQS)
Resolution:
4.50Å     R-factor:   0.223     R-free:   0.254
Authors: M.Pioletti,F.Schluenzen,J.Harms,R.Zarivach,M.Gluehmann, H.Avila,H.Bartels,C.Jacobi,T.Hartsch,A.Yonath,F.Franceschi
Key ref:
M.Pioletti et al. (2001). Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J, 20, 1829-1839. PubMed id: 11296217 DOI: 10.1093/emboj/20.8.1829
Date:
18-Mar-01     Release date:   12-Apr-01    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
249 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
156 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
82 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 17 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     8 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/20.8.1829 EMBO J 20:1829-1839 (2001)
PubMed id: 11296217  
 
 
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
M.Pioletti, F.Schlünzen, J.Harms, R.Zarivach, M.Glühmann, H.Avila, A.Bashan, H.Bartels, T.Auerbach, C.Jacobi, T.Hartsch, A.Yonath, F.Franceschi.
 
  ABSTRACT  
 
The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (A) Stereo view of the 3.2 structure of the 30S ribosomal subunit. The binding sites of tetracycline and edeine are indicated. Ribosomal proteins interacting with tetracycline have been colored and labeled. (B and C) Stereo views of the electron density map of two regions of the 3.2 structure, corresponding to helix 16 (H16) and ribosomal protein S16, respectively.
Figure 2.
Figure 2 Details of the binding sites of tetracycline and edeine. All images show the A weighted difference density at contour levels ranging from 3.2 to 2.2 for tetracycline, and 3.2 for both edeine and the RNA base pair induced upon its binding. (A) Stereo view of Tet-1. (B) Mono view of Tet-2. (C) Mono view of Tet-3. (D) Stereo view of Tet-4 and -6. (E) Left: stereo view of Tet-5. Right: chemical structure of tetracycline. (F) Left: stereo view of the binding site of edeine. Right: chemical structure of edeine.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 1829-1839) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21402075 G.Volkers, G.J.Palm, M.S.Weiss, G.D.Wright, and W.Hinrichs (2011).
Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase.
  FEBS Lett, 585, 1061-1066.
PDB codes: 2xdo 2xyo 2y6q 2y6r
20034956 A.A.Malygin, and G.G.Karpova (2010).
Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively.
  Nucleic Acids Res, 38, 2089-2098.  
20024973 D.Balenci, N.D'Amelio, E.Gaggelli, N.Gaggelli, L.Cellai, E.Molteni, and G.Valensin (2010).
Structural features of apramycin bound at the bacterial ribosome a site as detected by NMR and CD spectroscopy.
  Chembiochem, 11, 166-169.  
20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
Structural signatures of antibiotic binding sites on the ribosome.
  Nucleic Acids Res, 38, 5982-5994.  
20208344 H.Nanamiya, and F.Kawamura (2010).
Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis.
  Biosci Biotechnol Biochem, 74, 451-461.  
20551974 K.J.Simmons, I.Chopra, and C.W.Fishwick (2010).
Structure-based discovery of antibacterial drugs.
  Nat Rev Microbiol, 8, 501-510.  
20410587 K.W.Shimotohno, F.Kawamura, Y.Natori, H.Nanamiya, J.Magae, H.Ogata, T.Endo, T.Suzuki, and H.Yamaki (2010).
Inhibition of septation in Bacillus subtilis by a peptide antibiotic, edeine B(1).
  Biol Pharm Bull, 33, 568-571.  
20500856 S.Briolant, L.Almeras, M.Belghazi, E.Boucomont-Chapeaublanc, N.Wurtz, A.Fontaine, S.Granjeaud, T.Fusaï, C.Rogier, and B.Pradines (2010).
Plasmodium falciparum proteome changes in response to doxycycline treatment.
  Malar J, 9, 141.  
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.  
19493673 A.G.Myasnikov, A.Simonetti, S.Marzi, and B.P.Klaholz (2009).
Structure-function insights into prokaryotic and eukaryotic translation initiation.
  Curr Opin Struct Biol, 19, 300-309.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19661407 E.Breukink (2009).
Cell biology. Lethal traffic jam.
  Science, 325, 684-685.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19472250 P.Wang, W.Zhang, J.Zhan, and Y.Tang (2009).
Identification of OxyE as an ancillary oxygenase during tetracycline biosynthesis.
  Chembiochem, 10, 1544-1550.  
19595714 R.A.Marshall, C.E.Aitken, and J.D.Puglisi (2009).
GTP hydrolysis by IF2 guides progression of the ribosome into elongation.
  Mol Cell, 35, 37-47.  
19047651 S.Briolant, M.Baragatti, P.Parola, F.Simon, A.Tall, C.Sokhna, P.Hovette, M.M.Mamfoumbi, J.L.Koeck, J.Delmont, A.Spiegel, J.Castello, J.P.Gardair, J.F.Trape, M.Kombila, P.Minodier, T.Fusai, C.Rogier, and B.Pradines (2009).
Multinormal in vitro distribution model suitable for the distribution of Plasmodium falciparum chemosusceptibility to doxycycline.
  Antimicrob Agents Chemother, 53, 688-695.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19561193 Y.Yu, A.Marintchev, V.G.Kolupaeva, A.Unbehaun, T.Veryasova, S.C.Lai, P.Hong, G.Wagner, C.U.Hellen, and T.V.Pestova (2009).
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
  Nucleic Acids Res, 37, 5167-5182.  
18177894 A.A.Saraiya, T.N.Lamichhane, C.S.Chow, J.SantaLucia, and P.R.Cunningham (2008).
Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.
  J Mol Biol, 376, 645-657.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18443626 B.Zakeri, and G.D.Wright (2008).
Chemical biology of tetracycline antibiotics.
  Biochem Cell Biol, 86, 124-136.  
19053822 C.Sun, Q.Wang, J.D.Brubaker, P.M.Wright, C.D.Lerner, K.Noson, M.Charest, D.R.Siegel, Y.M.Wang, and A.G.Myers (2008).
A robust platform for the synthesis of new tetracycline antibiotics.
  J Am Chem Soc, 130, 17913-17927.  
18548290 G.J.Palm, T.Lederer, P.Orth, W.Saenger, M.Takahashi, W.Hillen, and W.Hinrichs (2008).
Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex.
  J Biol Inorg Chem, 13, 1097-1110.
PDB codes: 2fj1 2vke
18625614 H.David-Eden, and Y.Mandel-Gutfreund (2008).
Revealing unique properties of the ribosome using a network based analysis.
  Nucleic Acids Res, 36, 4641-4652.  
18940672 H.Xiao, T.E.Edwards, and A.R.Ferré-D'Amaré (2008).
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.
  Chem Biol, 15, 1125-1137.
PDB code: 3egz
18056078 M.E.Haque, D.Grasso, and L.L.Spremulli (2008).
The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt.
  Nucleic Acids Res, 36, 589-597.  
18211890 P.Aliprandi, C.Sizun, J.Perez, F.Mareuil, S.Caputo, J.L.Leroy, B.Odaert, S.Laalami, M.Uzan, and F.Bontems (2008).
S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis.
  J Biol Chem, 283, 13289-13301.  
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
18201347 R.A.Seymour, and S.D.Hogg (2008).
Antibiotics and chemoprophylaxis.
  Periodontol 2000, 46, 80.  
18941630 S.R.Starck, Y.Ow, V.Jiang, M.Tokuyama, M.Rivera, X.Qi, R.W.Roberts, and N.Shastri (2008).
A distinct translation initiation mechanism generates cryptic peptides for immune surveillance.
  PLoS ONE, 3, e3460.  
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.  
17244535 A.Fabbretti, C.L.Pon, S.P.Hennelly, W.E.Hill, J.S.Lodmell, and C.O.Gualerzi (2007).
The real-time path of translation factor IF3 onto and off the ribosome.
  Mol Cell, 25, 285-296.  
17268612 C.Hertweck, A.Luzhetskyy, Y.Rebets, and A.Bechthold (2007).
Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork.
  Nat Prod Rep, 24, 162-190.  
  17894445 C.S.Chow, T.N.Lamichhane, and S.K.Mahto (2007).
Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications.
  ACS Chem Biol, 2, 610-619.  
18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.
  Future Microbiol, 2, 571-574.  
17088492 G.Hirokawa, H.Kaji, and A.Kaji (2007).
Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin.
  Antimicrob Agents Chemother, 51, 175-180.  
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB codes: 2jq7 2nyo
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.  
17321546 S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, and P.B.Moore (2007).
The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
  J Mol Biol, 367, 1471-1479.
PDB codes: 2otj 2otl
17149559 Z.Czajgucki, M.Zimecki, and R.Andruszkiewicz (2007).
The immunoregulatory effects of edeine analogues in mice.
  Cell Mol Biol Lett, 12, 149-161.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
17021617 A.Mankin (2006).
Antibiotic blocks mRNA path on the ribosome.
  Nat Struct Mol Biol, 13, 858-860.  
16728979 A.Serganov, A.Polonskaia, A.T.Phan, R.R.Breaker, and D.J.Patel (2006).
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
  Nature, 441, 1167-1171.
PDB code: 2gdi
16517972 D.Hasenöhrl, D.Benelli, A.Barbazza, P.Londei, and U.Bläsi (2006).
Sulfolobus solfataricus translation initiation factor 1 stimulates translation initiation complex formation.
  RNA, 12, 674-682.  
16377719 E.T.Buurman, K.D.Johnson, R.K.Kelly, and K.MacCormack (2006).
Different modes of action of naphthyridones in gram-positive and gram-negative bacteria.
  Antimicrob Agents Chemother, 50, 385-387.  
16998488 F.Schluenzen, C.Takemoto, D.N.Wilson, T.Kaminishi, J.M.Harms, K.Hanawa-Suetsugu, W.Szaflarski, M.Kawazoe, M.Shirouzu, M.Shirouzo, K.H.Nierhaus, S.Yokoyama, and P.Fucini (2006).
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
  Nat Struct Mol Biol, 13, 871-878.
PDB code: 2hhh
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.
  EMBO J, 25, 196-210.  
16476727 K.Higashi, K.Kashiwagi, S.Taniguchi, Y.Terui, K.Yamamoto, A.Ishihama, and K.Igarashi (2006).
Enhancement of +1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli.
  J Biol Chem, 281, 9527-9537.  
16380421 L.Brandi, A.Fabbretti, A.La Teana, M.Abbondi, D.Losi, S.Donadio, and C.O.Gualerzi (2006).
Specific, efficient, and selective inhibition of prokaryotic translation initiation by a novel peptide antibiotic.
  Proc Natl Acad Sci U S A, 103, 39-44.  
16699167 L.Brandi, A.Fabbretti, M.Di Stefano, A.Lazzarini, M.Abbondi, and C.O.Gualerzi (2006).
Characterization of GE82832, a peptide inhibitor of translocation interacting with bacterial 30S ribosomal subunits.
  RNA, 12, 1262-1270.  
16707663 M.Müller, J.E.Weigand, O.Weichenrieder, and B.Suess (2006).
Thermodynamic characterization of an engineered tetracycline-binding riboswitch.
  Nucleic Acids Res, 34, 2607-2617.  
16723578 M.W.Olson, A.Ruzin, E.Feyfant, T.S.Rush, J.O'Connell, and P.A.Bradford (2006).
Functional, biophysical, and structural bases for antibacterial activity of tigecycline.
  Antimicrob Agents Chemother, 50, 2156-2166.  
16807065 P.E.Sum (2006).
Case studies in current drug development: 'glycylcyclines'.
  Curr Opin Chem Biol, 10, 374-379.  
17455787 P.Palecková, J.Bobek, J.Felsberg, and K.Mikulík (2006).
Activity of translation system and abundance of tmRNA during development of Streptomyces aureofaciens producing tetracycline.
  Folia Microbiol (Praha), 51, 517-524.  
17057344 S.E.Heffron, S.Mui, A.Aorora, K.Abel, E.Bergmann, and F.Jurnak (2006).
Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.
  Acta Crystallogr D Biol Crystallogr, 62, 1392-1400.
PDB codes: 2hcj 2hdn
16600874 S.M.Studer, and S.Joseph (2006).
Unfolding of mRNA secondary structure by the bacterial translation initiation complex.
  Mol Cell, 22, 105-115.  
16462810 T.V.Pestova, and C.U.Hellen (2006).
Translation, interrupted.
  Nat Struct Mol Biol, 13, 98-99.  
16847816 Z.Czajgucki, R.Andruszkiewicz, and W.Kamysz (2006).
Structure activity relationship studies on the antimicrobial activity of novel edeine A and D analogues.
  J Pept Sci, 12, 653-662.  
15876367 A.R.Cukras, and R.Green (2005).
Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
  J Mol Biol, 349, 47-59.  
16269538 A.Yassin, K.Fredrick, and A.S.Mankin (2005).
Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics.
  Proc Natl Acad Sci U S A, 102, 16620-16625.  
16180279 A.Yonath (2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
  Annu Rev Biochem, 74, 649-679.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
  Biol Chem, 386, 1239-1252.  
15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
  Annu Rev Biochem, 74, 129-177.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
15855511 L.L.Shen, C.Black-Schaefer, Y.Cai, P.J.Dandliker, and B.A.Beutel (2005).
Mechanism of action of a novel series of naphthyridine-type ribosome inhibitors: enhancement of tRNA footprinting at the decoding site of 16S rRNA.
  Antimicrob Agents Chemother, 49, 1890-1897.  
15901694 L.Nonaka, S.R.Connell, and D.E.Taylor (2005).
16S rRNA mutations that confer tetracycline resistance in Helicobacter pylori decrease drug binding in Escherichia coli ribosomes.
  J Bacteriol, 187, 3708-3712.  
15831754 M.G.Charest, C.D.Lerner, J.D.Brubaker, D.R.Siegel, and A.G.Myers (2005).
A convergent enantioselective route to structurally diverse 6-deoxytetracycline antibiotics.
  Science, 308, 395-398.  
16177132 N.M.Abdi, and K.Fredrick (2005).
Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli.
  RNA, 11, 1624-1632.  
16272105 P.B.Moore (2005).
Structural biology. A ribosomal coup: E. coli at last!
  Science, 310, 793-795.  
15792738 R.E.Hancock (2005).
Mechanisms of action of newer antibiotics for Gram-positive pathogens.
  Lancet Infect Dis, 5, 209-218.  
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
15352034 C.Braumann, W.Henke, C.A.Jacobi, and W.Dubiel (2004).
The tumor-suppressive reagent taurolidine is an inhibitor of protein biosynthesis.
  Int J Cancer, 112, 225-230.  
15554968 F.Schlünzen, E.Pyetan, P.Fucini, A.Yonath, and J.M.Harms (2004).
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.
  Mol Microbiol, 54, 1287-1294.
PDB code: 1xbp
15466596 H.Himeno, K.Hanawa-Suetsugu, T.Kimura, K.Takagi, W.Sugiyama, S.Shirata, T.Mikami, F.Odagiri, Y.Osanai, D.Watanabe, S.Goto, L.Kalachnyuk, C.Ushida, and A.Muto (2004).
A novel GTPase activated by the small subunit of ribosome.
  Nucleic Acids Res, 32, 5303-5309.  
15688524 J.L.Simala-Grant, and D.E.Taylor (2004).
Molecular biology methods for the characterization of Helicobacter pylori infections and their diagnosis.
  APMIS, 112, 886-897.  
15059283 J.M.Harms, F.Schlünzen, P.Fucini, H.Bartels, and A.Yonath (2004).
Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin.
  BMC Biol, 2, 4.
PDB code: 1sm1
15534366 J.Thompson, and A.E.Dahlberg (2004).
Testing the conservation of the translational machinery over evolution in diverse environments: assaying Thermus thermophilus ribosomes and initiation factors in a coupled transcription-translation system from Escherichia coli.
  Nucleic Acids Res, 32, 5954-5961.  
15507686 K.Kasai, T.Kanno, Y.Endo, K.Wakasa, and Y.Tozawa (2004).
Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline.
  Nucleic Acids Res, 32, 5732-5741.  
15141029 M.M.Anokhina, A.Barta, K.H.Nierhaus, V.A.Spiridonova, and A.M.Kopylov (2004).
Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli.
  Nucleic Acids Res, 32, 2594-2597.  
14769948 O.Novac, A.S.Guenier, and J.Pelletier (2004).
Inhibitors of protein synthesis identified by a high throughput multiplexed translation screen.
  Nucleic Acids Res, 32, 902-915.  
15491801 T.Auerbach, A.Bashan, and A.Yonath (2004).
Ribosomal antibiotics: structural basis for resistance, synergism and selectivity.
  Trends Biotechnol, 22, 570-576.  
15337844 Z.Druzina, and B.S.Cooperman (2004).
Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center.
  RNA, 10, 1550-1562.  
12925991 A.Bashan, R.Zarivach, F.Schluenzen, I.Agmon, J.Harms, T.Auerbach, D.Baram, R.Berisio, H.Bartels, H.A.Hansen, P.Fucini, D.Wilson, M.Peretz, M.Kessler, and A.Yonath (2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
  Biopolymers, 70, 19-41.  
14669983 A.Yonath (2003).
Ribosomal tolerance and peptide bond formation.
  Biol Chem, 384, 1411-1419.  
14627814 C.C.Correll, J.Beneken, M.J.Plantinga, M.Lubbers, and Y.L.Chan (2003).
The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure.
  Nucleic Acids Res, 31, 6806-6818.
PDB codes: 1q93 1q96 1q9a
15040181 C.Walsh (2003).
Where will new antibiotics come from?
  Nat Rev Microbiol, 1, 65-70.  
12554858 E.P.Plant, K.L.Jacobs, J.W.Harger, A.Meskauskas, J.L.Jacobs, J.L.Baxter, A.N.Petrov, and J.D.Dinman (2003).
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
  RNA, 9, 168-174.  
12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
  Biopolymers, 68, 234-249.  
14561879 I.S.Gabashvili, M.Whirl-Carrillo, M.Bada, D.R.Banatao, and R.B.Altman (2003).
Ribosomal dynamics inferred from variations in experimental measurements.
  RNA, 9, 1301-1307.  
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.  
14523919 Q.Vicens, and E.Westhof (2003).
RNA as a drug target: the case of aminoglycosides.
  Chembiochem, 4, 1018-1023.  
12869707 S.Marzi, W.Knight, L.Brandi, E.Caserta, N.Soboleva, W.E.Hill, C.O.Gualerzi, and J.S.Lodmell (2003).
Ribosomal localization of translation initiation factor IF2.
  RNA, 9, 958-969.  
12574130 S.R.Connell, C.A.Trieber, G.P.Dinos, E.Einfeldt, D.E.Taylor, and K.H.Nierhaus (2003).
Mechanism of Tet(O)-mediated tetracycline resistance.
  EMBO J, 22, 945-953.  
14638464 S.R.Connell, D.M.Tracz, K.H.Nierhaus, and D.E.Taylor (2003).
Ribosomal protection proteins and their mechanism of tetracycline resistance.
  Antimicrob Agents Chemother, 47, 3675-3681.  
12925990 T.Hermann (2003).
Chemical and functional diversity of small molecule ligands for RNA.
  Biopolymers, 70, 4.  
12486074 W.L.Ng, K.M.Kazmierczak, G.T.Robertson, R.Gilmour, and M.E.Winkler (2003).
Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors.
  J Bacteriol, 185, 359-370.  
12930962 X.J.Lu, and W.K.Olson (2003).
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
  Nucleic Acids Res, 31, 5108-5121.  
11988470 A.Yonath (2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
  Annu Rev Biophys Biomol Struct, 31, 257-273.  
11914344 C.A.Trieber, and D.E.Taylor (2002).
Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline.
  J Bacteriol, 184, 2131-2140.  
12435699 D.Dailidiene, M.T.Bertoli, J.Miciuleviciene, A.K.Mukhopadhyay, G.Dailide, M.A.Pascasio, L.Kupcinskas, and D.E.Berg (2002).
Emergence of tetracycline resistance in Helicobacter pylori: multiple mutational changes in 16S ribosomal DNA and other genetic loci.
  Antimicrob Agents Chemother, 46, 3940-3946.  
12095986 E.C.Koc, and L.L.Spremulli (2002).
Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs.
  J Biol Chem, 277, 35541-35549.  
12087167 I.Amarantos, I.K.Zarkadis, and D.L.Kalpaxis (2002).
The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
  Nucleic Acids Res, 30, 2832-2843.  
12150912 J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, and T.A.Steitz (2002).
The structures of four macrolide antibiotics bound to the large ribosomal subunit.
  Mol Cell, 10, 117-128.
PDB codes: 1k8a 1k9m 1kd1 1m1k
11867615 M.A.Schäfer, A.O.Tastan, S.Patzke, G.Blaha, C.M.Spahn, D.N.Wilson, and K.H.Nierhaus (2002).
Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
  J Biol Chem, 277, 19095-19105.  
12403465 M.Carriere, V.Vijayabaskar, D.Applefield, I.Harvey, P.Garneau, J.Lorsch, A.Lapidot, and J.Pelletier (2002).
Inhibition of protein synthesis by aminoglycoside-arginine conjugates.
  RNA, 8, 1267-1279.  
11784311 M.Hertweck, R.Hiller, and M.W.Mueller (2002).
Inhibition of nuclear pre-mRNA splicing by antibiotics in vitro.
  Eur J Biochem, 269, 175-183.  
12183259 M.M.Gerrits, M.R.de Zoete, N.L.Arents, E.J.Kuipers, and J.G.Kusters (2002).
16S rRNA mutation-mediated tetracycline resistance in Helicobacter pylori.
  Antimicrob Agents Chemother, 46, 2996-3000.  
12354218 S.R.Connell, C.A.Trieber, U.Stelzl, E.Einfeldt, D.E.Taylor, and K.H.Nierhaus (2002).
The tetracycline resistance protein Tet(o) perturbs the conformation of the ribosomal decoding centre.
  Mol Microbiol, 45, 1463-1472.  
11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
  Cell, 108, 557-572.  
12762007 A.Bashan, I.Agmon, R.Zarivach, F.Schluenzen, J.Harms, M.Pioletti, H.Bartels, M.Gluehmann, H.Hansen, T.Auerbach, F.Franceschi, and A.Yonath (2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
  Cold Spring Harb Symp Quant Biol, 66, 43-56.  
11701127 C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, and J.Frank (2001).
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
  Cell, 107, 373-386.
PDB codes: 1k5x 1k5y
12762039 C.O.Gualerzi, L.Brandi, E.Caserta, C.Garofalo, M.Lammi, A.La Teana, D.Petrelli, R.Spurio, J.Tomsic, and C.L.Pon (2001).
Initiation factors in the early events of mRNA translation in bacteria.
  Cold Spring Harb Symp Quant Biol, 66, 363-376.  
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.  
11500382 D.Petrelli, A.LaTeana, C.Garofalo, R.Spurio, C.L.Pon, and C.O.Gualerzi (2001).
Translation initiation factor IF3: two domains, five functions, one mechanism?
  EMBO J, 20, 4560-4569.  
11566123 G.M.Culver (2001).
Meanderings of the mRNA through the ribosome.
  Structure, 9, 751-758.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
12762011 P.Sergiev, A.Leonov, S.Dokudovskaya, O.Shpanchenko, O.Dontsova, A.Bogdanov, J.Rinke-Appel, F.Mueller, M.Osswald, K.von Knoblauch, and R.Brimacombe (2001).
Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome.
  Cold Spring Harb Symp Quant Biol, 66, 87.  
12762032 S.Shuman (2001).
The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny.
  Cold Spring Harb Symp Quant Biol, 66, 301-312.  
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.