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PDBsum entry 1hnw

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1hnw
Jmol
Contents
Protein chains
234 a.a. *
206 a.a. *
208 a.a. *
150 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
98 a.a. *
119 a.a. *
124 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
88 a.a. *
104 a.a. *
73 a.a. *
80 a.a. *
99 a.a. *
24 a.a. *
DNA/RNA
Ligands
TAC ×2
Metals
_MG ×96
_ZN ×2
* Residue conservation analysis
PDB id:
1hnw
Name: Ribosome
Title: Structure of the thermus thermophilus 30s ribosomal subunit in complex with tetracycline
Structure: 16s ribosomal RNA. Chain: a. Fragment of messenger RNA. Chain: x. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: 22mer (from PQS)
Resolution:
3.40Å     R-factor:   0.222     R-free:   0.264
Authors: D.E.Brodersen,W.M.Clemons Jr.,A.P.Carter,R.Morgan-Warren, B.T.Wimberly,V.Ramakrishnan
Key ref:
D.E.Brodersen et al. (2000). The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell, 103, 1143-1154. PubMed id: 11163189 DOI: 10.1016/S0092-8674(00)00216-6
Date:
08-Dec-00     Release date:   21-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
234 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.
150 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.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 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.
73 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  CATH domain
* 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     8 terms  

 

 
DOI no: 10.1016/S0092-8674(00)00216-6 Cell 103:1143-1154 (2000)
PubMed id: 11163189  
 
 
The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit.
D.E.Brodersen, W.M.Clemons, A.P.Carter, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan.
 
  ABSTRACT  
 
We have used the recently determined atomic structure of the 30S ribosomal subunit to determine the structures of its complexes with the antibiotics tetracycline, pactamycin, and hygromycin B. The antibiotics bind to discrete sites on the 30S subunit in a manner consistent with much but not all biochemical data. For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overview of Tetracycline, Pactamycin, and Hygromycin B in the 30S SubunitAntibiotics are shown as space-filling models, with tetracycline (blue), pactamycin (green), and hygromycin B (red). The parts of 16S RNA that make contacts with any of the three antibiotics are colored as in the following figures.
Figure 2.
Figure 2. Tetracycline(a) Stereo figure of the primary Tc binding site (A site region) with rings A, B, C, and D of the fused-ring system. H34 (top left, blue) and H31 (top right, green) are shown together with H44 (cyan). The enhanced reactivity of C1054 (green sphere) and the reduced UV cross-link C967xC1400 (dashed red line) are indicated. The bound magnesium ion (gold sphere) is shown with residues involved in its coordination (thick sticks, light blue). The initial difference electron density map (mF[o]-DF[c]), calculated before inclusion of Tc in the model, is shown at 6σ.(b) Overview of primary binding site of Tc indicating the RNA components close to the site and the interaction with A site tRNA, H34 (blue), H31 (green), H18 (orange), and H44 (cyan). The model of A site tRNA (red) and mRNA (yellow) is shown.(c) Chemical structure diagram of Tc and possible interactions with 16S RNA at the primary site (blue). The shaded area represents positions on the molecule that can be modified without affecting its inhibitory action ([31]).(d) Stereo figure of the secondary tetracycline site (H27 switch region) with rings A, B, C, and D. H27 is yellow/green/red and H11 violet. The 885–887:910–912 base pairs are shown in red, whereas the bases 888–890, involved in a proposed alternative base-pairing scheme are green. The reduced reactivity towards DMS at A892 (red sphere) and the reduced cross-link G894-U244 (red dashed line) are also shown. The initial difference electron density map (mF[o]-DF[c]) is shown at 4σ.(e) Overview of secondary binding site of Tc along with the RNA elements it interacts with, H11 (violet), H27 (yellow, red, and green as above).(f) Possible hydrogen bond interactions with 16S RNA at the secondary tetracycline binding site (blue).
 
  The above figures are reprinted by permission from Cell Press: Cell (2000, 103, 1143-1154) copyright 2000.  
  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
21513878 W.Lu, N.Roongsawang, and T.Mahmud (2011).
Biosynthetic studies and genetic engineering of pactamycin analogs with improved selectivity toward malarial parasites.
  Chem Biol, 18, 425-431.  
20661497 B.Carlotti, D.Fuoco, and F.Elisei (2010).
Fast and ultrafast spectroscopic investigation of tetracycline derivatives in organic and aqueous media.
  Phys Chem Chem Phys, 12, 15580-15591.  
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
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.  
20661239 K.Otoguro, M.Iwatsuki, A.Ishiyama, M.Namatame, A.Nishihara-Tukashima, S.Shibahara, S.Kondo, H.Yamada, and S.Omura (2010).
Promising lead compounds for novel antiprotozoals.
  J Antibiot (Tokyo), 63, 381-384.  
20696400 M.A.Arbing, S.K.Handelman, A.P.Kuzin, G.Verdon, C.Wang, M.Su, F.P.Rothenbacher, M.Abashidze, M.Liu, J.M.Hurley, R.Xiao, T.Acton, M.Inouye, G.T.Montelione, N.A.Woychik, and J.F.Hunt (2010).
Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.
  Structure, 18, 996.
PDB codes: 2h28 2ict 2inw 3kh2
20835226 M.H.Bengtson, and C.A.Joazeiro (2010).
Role of a ribosome-associated E3 ubiquitin ligase in protein quality control.
  Nature, 467, 470-473.  
20094751 M.Morozumi, T.Takahashi, and K.Ubukata (2010).
Macrolide-resistant Mycoplasma pneumoniae: characteristics of isolates and clinical aspects of community-acquired pneumonia.
  J Infect Chemother, 16, 78-86.  
20215440 S.M.Dibrov, J.Parsons, and T.Hermann (2010).
A model for the study of ligand binding to the ribosomal RNA helix h44.
  Nucleic Acids Res, 38, 4458-4465.
PDB code: 3loa
20406434 T.M.Bakheet, and A.J.Doig (2010).
Properties and identification of antibiotic drug targets.
  BMC Bioinformatics, 11, 195.  
20154667 T.Schneider-Poetsch, T.Usui, D.Kaida, and M.Yoshida (2010).
Garbled messages and corrupted translations.
  Nat Chem Biol, 6, 189-198.  
18615434 A.Aleksandrov, and T.Simonson (2009).
Molecular mechanics models for tetracycline analogs.
  J Comput Chem, 30, 243-255.  
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.  
19258531 B.A.Maguire (2009).
Inhibition of bacterial ribosome assembly: a suitable drug target?
  Microbiol Mol Biol Rev, 73, 22-35.  
19553343 B.Llano-Sotelo, R.P.Hickerson, L.Lancaster, H.F.Noller, and A.S.Mankin (2009).
Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.
  RNA, 15, 1597-1604.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19908837 L.B.Pickens, W.Kim, P.Wang, H.Zhou, K.Watanabe, S.Gomi, and Y.Tang (2009).
Biochemical analysis of the biosynthetic pathway of an anticancer tetracycline SF2575.
  J Am Chem Soc, 131, 17677-17689.  
19007902 L.B.Pickens, and Y.Tang (2009).
Decoding and engineering tetracycline biosynthesis.
  Metab Eng, 11, 69-75.  
19666721 N.Van Dyke, B.F.Pickering, and M.W.Van Dyke (2009).
Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation.
  Nucleic Acids Res, 37, 6116-6125.  
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.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19670201 T.Ito, N.Roongsawang, N.Shirasaka, W.Lu, P.M.Flatt, N.Kasanah, C.Miranda, and T.Mahmud (2009).
Deciphering pactamycin biosynthesis and engineered production of new pactamycin analogues.
  Chembiochem, 10, 2253-2265.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
19908830 Y.Xie, A.V.Dix, and Y.Tor (2009).
FRET enabled real time detection of RNA-small molecule binding.
  J Am Chem Soc, 131, 17605-17614.  
19124462 Y.Zhang, and M.Inouye (2009).
The Inhibitory Mechanism of Protein Synthesis by YoeB, an Escherichia coli Toxin.
  J Biol Chem, 284, 6627-6638.  
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.  
18443626 B.Zakeri, and G.D.Wright (2008).
Chemical biology of tetracycline antibiotics.
  Biochem Cell Biol, 86, 124-136.  
18060665 C.Foster, and W.S.Champney (2008).
Characterization of a 30S ribosomal subunit assembly intermediate found in Escherichia coli cells growing with neomycin or paromomycin.
  Arch Microbiol, 189, 441-449.  
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.  
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
18567815 M.A.Borovinskaya, S.Shoji, K.Fredrick, and J.H.Cate (2008).
Structural basis for hygromycin B inhibition of protein biosynthesis.
  RNA, 14, 1590-1599.
PDB codes: 3df1 3df2 3df3 3df4
18398006 M.Liu, Y.Zhang, M.Inouye, and N.A.Woychik (2008).
Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit.
  Proc Natl Acad Sci U S A, 105, 5885-5890.  
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
18518820 R.A.Marshall, C.E.Aitken, M.Dorywalska, and J.D.Puglisi (2008).
Translation at the single-molecule level.
  Annu Rev Biochem, 77, 177-203.  
18201347 R.A.Seymour, and S.D.Hogg (2008).
Antibiotics and chemoprophylaxis.
  Periodontol 2000, 46, 80.  
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.  
18052610 A.F.Palazzo, M.Springer, Y.Shibata, C.S.Lee, A.P.Dias, and T.A.Rapoport (2007).
The signal sequence coding region promotes nuclear export of mRNA.
  PLoS Biol, 5, e322.  
17264995 B.Verma, R.D.Robarts, and J.V.Headley (2007).
Impacts of tetracycline on planktonic bacterial production in prairie aquatic systems.
  Microb Ecol, 54, 52-55.  
18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.
  Future Microbiol, 2, 571-574.  
17827660 F.Kudo, Y.Kasama, T.Hirayama, and T.Eguchi (2007).
Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation.
  J Antibiot (Tokyo), 60, 492-503.  
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
17209036 H.Yamamoto, N.Nakashima, Y.Ikeda, and T.Uchiumi (2007).
Binding mode of the first aminoacyl-tRNA in translation initiation mediated by Plautia stali intestine virus internal ribosome entry site.
  J Biol Chem, 282, 7770-7776.  
17905922 H.Zhou, H.Hu, L.Zhang, R.Li, H.Ouyang, J.Ming, and C.Jin (2007).
O-Mannosyltransferase 1 in Aspergillus fumigatus (AfPmt1p) is crucial for cell wall integrity and conidium morphology, especially at an elevated temperature.
  Eukaryot Cell, 6, 2260-2268.  
17234428 I.Dalmázio, M.O.Almeida, R.Augusti, and T.M.Alves (2007).
Monitoring the degradation of tetracycline by ozone in aqueous medium via atmospheric pressure ionization mass spectrometry.
  J Am Soc Mass Spectrom, 18, 679-687.  
17502914 J.M.Yang, Y.F.Chen, Y.Y.Tu, K.R.Yen, and Y.L.Yang (2007).
Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors.
  PLoS ONE, 2, e428.  
16892199 J.Zhou, G.Wang, L.H.Zhang, and X.S.Ye (2007).
Modifications of aminoglycoside antibiotics targeting RNA.
  Med Res Rev, 27, 279-316.  
17187988 K.Y.Sanbonmatsu, and C.S.Tung (2007).
High performance computing in biology: multimillion atom simulations of nanoscale systems.
  J Struct Biol, 157, 470-480.  
17530725 M.Schlitzer (2007).
Malaria Chemotherapeutics Part I: History of Antimalarial Drug Development, Currently Used Therapeutics, and Drugs in Clinical Development.
  ChemMedChem, 2, 944-986.  
18033580 N.Dixon, L.S.Wong, T.H.Geerlings, and J.Micklefield (2007).
Cellular targets of natural products.
  Nat Prod Rep, 24, 1288-1310.  
17942426 S.Bernacchi, S.Freisz, C.Maechling, B.Spiess, R.Marquet, P.Dumas, and E.Ennifar (2007).
Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion.
  Nucleic Acids Res, 35, 7128-7139.  
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
17043113 S.M.McGaha, and W.S.Champney (2007).
Hygromycin B inhibition of protein synthesis and ribosome biogenesis in Escherichia coli.
  Antimicrob Agents Chemother, 51, 591-596.  
17319662 V.K.Tam, D.Kwong, and Y.Tor (2007).
Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery.
  J Am Chem Soc, 129, 3257-3266.  
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
16990269 A.Kubarenko, P.Sergiev, W.Wintermeyer, O.Dontsova, and M.V.Rodnina (2006).
Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome.
  J Biol Chem, 281, 35235-35244.  
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
16495252 B.L.Makepeace, L.Rodgers, and A.J.Trees (2006).
Rate of elimination of Wolbachia pipientis by doxycycline in vitro increases following drug withdrawal.
  Antimicrob Agents Chemother, 50, 922-927.  
17129165 C.Hyeon, R.I.Dima, and D.Thirumalai (2006).
Size, shape, and flexibility of RNA structures.
  J Chem Phys, 125, 194905.  
16717405 H.Yoneyama, and R.Katsumata (2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
  Biosci Biotechnol Biochem, 70, 1060-1075.  
16915600 K.F.Blount, and Y.Tor (2006).
A tale of two targets: differential RNA selectivity of nucleobase-aminoglycoside conjugates.
  Chembiochem, 7, 1612-1621.  
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.  
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.  
17067919 M.M.Gerrits, A.H.van Vliet, E.J.Kuipers, and J.G.Kusters (2006).
Helicobacter pylori and antimicrobial resistance: molecular mechanisms and clinical implications.
  Lancet Infect Dis, 6, 699-709.  
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.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
16788184 P.B.Lodato, E.J.Rogers, and P.S.Lovett (2006).
A variation of the translation attenuation model can explain the inducible regulation of the pBC16 tetracycline resistance gene in Bacillus subtilis.
  J Bacteriol, 188, 4749-4758.  
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
17189194 S.Shoji, S.E.Walker, and K.Fredrick (2006).
Reverse translocation of tRNA in the ribosome.
  Mol Cell, 24, 931-942.  
16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.
  Mol Microbiol, 59, 1664-1677.  
16180279 A.Yonath (2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
  Annu Rev Biochem, 74, 649-679.  
15831747 C.Khosla, and Y.Tang (2005).
Chemistry. A new route to designer antibiotics.
  Science, 308, 367-368.  
15568198 D.Vourloumis, G.C.Winters, K.B.Simonsen, M.Takahashi, B.K.Ayida, S.Shandrick, Q.Zhao, Q.Han, and T.Hermann (2005).
Aminoglycoside-hybrid ligands targeting the ribosomal decoding site.
  Chembiochem, 6, 58-65.  
16096836 J.A.Silvers, and W.S.Champney (2005).
Accumulation and turnover of 23S ribosomal RNA in azithromycin-inhibited ribonuclease mutant strains of Escherichia coli.
  Arch Microbiol, 184, 66-77.  
16111914 J.A.Sutcliffe (2005).
Improving on nature: antibiotics that target the ribosome.
  Curr Opin Microbiol, 8, 534-542.  
15980485 J.Kleinjung, and F.Fraternali (2005).
POPSCOMP: an automated interaction analysis of biomolecular complexes.
  Nucleic Acids Res, 33, W342-W346.  
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.  
16189114 M.Hu, S.Nandi, C.Davies, and R.A.Nicholas (2005).
High-level chromosomally mediated tetracycline resistance in Neisseria gonorrhoeae results from a point mutation in the rpsJ gene encoding ribosomal protein S10 in combination with the mtrR and penB resistance determinants.
  Antimicrob Agents Chemother, 49, 4327-4334.  
16244134 M.N.Lambert, J.A.Hoerter, M.J.Pereira, and N.G.Walter (2005).
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.
  RNA, 11, 1688-1700.  
15670150 R.M.Knutsson Jenvert, and L.Holmberg Schiavone (2005).
Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli.
  FEBS J, 272, 685-695.  
15713840 S.Cherry, T.Doukas, S.Armknecht, S.Whelan, H.Wang, P.Sarnow, and N.Perrimon (2005).
Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition.
  Genes Dev, 19, 445-452.  
15769877 S.Hanson, G.Bauer, B.Fink, and B.Suess (2005).
Molecular analysis of a synthetic tetracycline-binding riboswitch.
  RNA, 11, 503-511.  
15995195 S.T.Gregory, J.F.Carr, D.Rodriguez-Correa, and A.E.Dahlberg (2005).
Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus.
  J Bacteriol, 187, 4804-4812.  
15643063 S.Y.Kim, and E.A.Craig (2005).
Broad sensitivity of Saccharomyces cerevisiae lacking ribosome-associated chaperone ssb or zuo1 to cations, including aminoglycosides.
  Eukaryot Cell, 4, 82-89.  
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
16041951 U.Holzgrabe (2005).
[New paths to highly effective tetracyclines]
  Pharm Unserer Zeit, 34, 258-259.  
16304156 Y.Zhou, V.E.Gregor, Z.Sun, B.K.Ayida, G.C.Winters, D.Murphy, K.B.Simonsen, D.Vourloumis, S.Fish, J.M.Froelich, D.Wall, and T.Hermann (2005).
Structure-guided discovery of novel aminoglycoside mimetics as antibacterial translation inhibitors.
  Antimicrob Agents Chemother, 49, 4942-4949.  
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.  
15593140 B.François, J.Szychowski, S.S.Adhikari, K.Pachamuthu, E.E.Swayze, R.H.Griffey, M.T.Migawa, E.Westhof, and S.Hanessian (2004).
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site.
  Angew Chem Int Ed Engl, 43, 6735-6738.
PDB codes: 2be0 2bee
15515129 C.N.Ionescu, S.Origanti, and M.A.McAlear (2004).
The yeast rRNA biosynthesis factor Ebp2p is also required for efficient nuclear division.
  Yeast, 21, 1219-1232.  
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.  
14999102 K.Das, T.Acton, Y.Chiang, L.Shih, E.Arnold, and G.T.Montelione (2004).
Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.
  Proc Natl Acad Sci U S A, 101, 4041-4046.
PDB code: 1p91
14734187 M.L.Ribeiro, M.M.Gerrits, Y.H.Benvengo, M.Berning, A.P.Godoy, E.J.Kuipers, S.Mendonça, A.H.van Vliet, J.Pedrazzoli, and J.G.Kusters (2004).
Detection of high-level tetracycline resistance in clinical isolates of Helicobacter pylori using PCR-RFLP.
  FEMS Immunol Med Microbiol, 40, 57-61.  
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.  
15174098 M.P.Quinlan (2004).
Vinculin, VASP, and profilin are coordinately regulated during actin remodeling in epithelial cells, which requires de novo protein synthesis and protein kinase signal transduction pathways.
  J Cell Physiol, 200, 277-290.  
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.  
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).
Three-dimensional structures of translating ribosomes by Cryo-EM.
  Mol Cell, 14, 57-66.  
15448679 S.C.Blanchard, R.L.Gonzalez, H.D.Kim, S.Chu, and J.D.Puglisi (2004).
tRNA selection and kinetic proofreading in translation.
  Nat Struct Mol Biol, 11, 1008-1014.  
15491801 T.Auerbach, A.Bashan, and A.Yonath (2004).
Ribosomal antibiotics: structural basis for resistance, synergism and selectivity.
  Trends Biotechnol, 22, 570-576.  
15295039 T.Konno, T.Takahashi, D.Kurita, A.Muto, and H.Himeno (2004).
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation.
  Nucleic Acids Res, 32, 4119-4126.  
15452119 W.Yang, I.F.Moore, K.P.Koteva, D.C.Bareich, D.W.Hughes, and G.D.Wright (2004).
TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics.
  J Biol Chem, 279, 52346-52352.  
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.  
12810914 A.Djikeng, H.Shi, C.Tschudi, S.Shen, and E.Ullu (2003).
An siRNA ribonucleoprotein is found associated with polyribosomes in Trypanosoma brucei.
  RNA, 9, 802-808.  
12907716 C.M.Duarte, L.M.Wadley, and A.M.Pyle (2003).
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
  Nucleic Acids Res, 31, 4755-4761.  
12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
  Biopolymers, 68, 234-249.  
12690106 J.R.Colca, W.G.McDonald, D.J.Waldon, L.M.Thomasco, R.C.Gadwood, E.T.Lund, G.S.Cavey, W.R.Mathews, L.D.Adams, E.T.Cecil, J.D.Pearson, J.H.Bock, J.E.Mott, D.L.Shinabarger, L.Xiong, and A.S.Mankin (2003).
Cross-linking in the living cell locates the site of action of oxazolidinone antibiotics.
  J Biol Chem, 278, 21972-21979.  
12939790 L.J.Ming (2003).
Structure and function of "metalloantibiotics".
  Med Res Rev, 23, 697-762.  
12709313 P.Pfister, M.Risch, D.E.Brodersen, and E.C.Böttger (2003).
Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.
  Antimicrob Agents Chemother, 47, 1496-1502.  
14523926 P.Pfister, S.Hobbie, Q.Vicens, E.C.Böttger, and E.Westhof (2003).
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures.
  Chembiochem, 4, 1078-1088.  
14523919 Q.Vicens, and E.Westhof (2003).
RNA as a drug target: the case of aminoglycosides.
  Chembiochem, 4, 1018-1023.  
12857776 S.B.Vakulenko, and S.Mobashery (2003).
Versatility of aminoglycosides and prospects for their future.
  Clin Microbiol Rev, 16, 430-450.  
12554856 S.Joseph (2003).
After the ribosome structure: how does translocation work?
  RNA, 9, 160-164.  
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.  
12821448 e.l.-.S.E.Habib, J.N.Scarsdale, and K.A.Reynolds (2003).
Biosynthetic origin of hygromycin A.
  Antimicrob Agents Chemother, 47, 2065-2071.  
11741992 A.Raney, G.L.Law, G.J.Mize, and D.R.Morris (2002).
Regulated translation termination at the upstream open reading frame in s-adenosylmethionine decarboxylase mRNA.
  J Biol Chem, 277, 5988-5994.  
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.  
11861649 C.Yarian, H.Townsend, W.Czestkowski, E.Sochacka, A.J.Malkiewicz, R.Guenther, A.Miskiewicz, and P.F.Agris (2002).
Accurate translation of the genetic code depends on tRNA modified nucleosides.
  J Biol Chem, 277, 16391-16395.  
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.  
11854489 I.Harvey, P.Garneau, and J.Pelletier (2002).
Forced engagement of a RNA/protein complex by a chemical inducer of dimerization to modulate gene expression.
  Proc Natl Acad Sci U S A, 99, 1882-1887.  
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
12490711 J.M.Zimmerman, and L.J.Maher (2002).
In vivo selection of spectinomycin-binding RNAs.
  Nucleic Acids Res, 30, 5425-5435.  
12270832 J.Ma, A.Campbell, and S.Karlin (2002).
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.
  J Bacteriol, 184, 5733-5745.  
12465030 K.B.Simonsen, B.K.Ayida, D.Vourloumis, M.Takahashi, G.C.Winters, S.Barluenga, S.Qamar, S.Shandrick, Q.Zhao, and T.Hermann (2002).
Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA.
  Chembiochem, 3, 1223-1228.  
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.  
12209000 M.C.Ganoza, M.C.Kiel, and H.Aoki (2002).
Evolutionary conservation of reactions in translation.
  Microbiol Mol Biol Rev, 66, 460.  
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.  
12358431 N.Böddeker, G.Bahador, C.Gibbs, E.Mabery, J.Wolf, L.Xu, and J.Watson (2002).
Characterization of a novel antibacterial agent that inhibits bacterial translation.
  RNA, 8, 1120-1128.  
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.  
12009887 S.Yoshizawa, D.Fourmy, R.G.Eason, and J.D.Puglisi (2002).
Sequence-specific recognition of the major groove of RNA by deoxystreptamine.
  Biochemistry, 41, 6263-6270.  
11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
  Cell, 108, 557-572.  
12458793 Y.G.Ren, J.Martínez, L.A.Kirsebom, and A.Virtanen (2002).
Inhibition of Klenow DNA polymerase and poly(A)-specific ribonuclease by aminoglycosides.
  RNA, 8, 1393-1400.  
11807047 Y.Wei, and D.H.Bechhofer (2002).
Tetracycline induces stabilization of mRNA in Bacillus subtilis.
  J Bacteriol, 184, 889-894.  
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.  
11290319 B.A.Maguire, and R.A.Zimmermann (2001).
The ribosome in focus.
  Cell, 104, 813-816.  
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.  
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.  
11557474 M.C.Ganoza, and M.C.Kiel (2001).
A ribosomal ATPase is a target for hygromycin B inhibition on Escherichia coli ribosomes.
  Antimicrob Agents Chemother, 45, 2813-2819.  
11296217 M.Pioletti, F.Schlünzen, J.Harms, R.Zarivach, M.Glühmann, H.Avila, A.Bashan, H.Bartels, T.Auerbach, C.Jacobi, T.Hartsch, A.Yonath, and F.Franceschi (2001).
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
  EMBO J, 20, 1829-1839.
PDB codes: 1i94 1i95 1i96 1i97
11258942 P.B.Moore (2001).
The ribosome at atomic resolution.
  Biochemistry, 40, 3243-3250.  
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.  
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
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.