PDBsum entry: 1fjg

Ribosome

PDB-id

1fjg

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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Description

Header details

Protein chains

DNA/RNA

Ligands

PAR

SCM

SRY

Metal ions

_MG ×96

_ZN ×2

* Residue conservation analysis

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PDB id:

1fjg

Name:

Ribosome

Title:

Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotics streptomycin, spectinomycin, and paromomycin

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

Biological unit:

22mer (from PQS)

UniProt:

Chain B: P80371 (RS2_THET8)

Seq:				256 a.a.

Struc:				237 a.a.

Chain C: P80372 (RS3_THET8)

Seq:				239 a.a.

Struc:				206 a.a.

Chain D: P80373 (RS4_THET8)

Seq:				209 a.a.

Struc:				208 a.a.*

Chain E: Q5SHQ5 (RS5_THET8)

Seq:				162 a.a.

Struc:				150 a.a.

Chain F: Q5SLP8 (RS6_THET8)

Seq:				101 a.a.

Struc:				101 a.a.

Chain G: P17291 (RS7_THET8)

Seq:				156 a.a.

Struc:				155 a.a.

Chain H: Q5SHQ2 (RS8_THET8)

Seq:				138 a.a.

Struc:				138 a.a.

Chain I: P80374 (RS9_THET8)

Seq:				128 a.a.

Struc:				127 a.a.*

Chain J: Q5SHN7 (RS10_THET8)

Seq:				105 a.a.

Struc:				98 a.a.

Chain K: P80376 (RS11_THET8)

Seq:				129 a.a.

Struc:				119 a.a.

Chain L: Q5SHN3 (RS12_THET8)

Seq:				132 a.a.

Struc:				125 a.a.

Chain M: P80377 (RS13_THET8)

Seq:				126 a.a.

Struc:				125 a.a.

Chain N: Q5SHQ1 (RS14Z_THET8)

Seq:				61 a.a.

Struc:				60 a.a.

Chain O: Q5SJ76 (RS15_THET8)

Seq:				89 a.a.

Struc:				88 a.a.

Chain P: Q5SJH3 (RS16_THET8)

Seq:				88 a.a.

Struc:				83 a.a.

Chain Q: Q5SHP7 (RS17_THET8)

Seq:				105 a.a.

Struc:				104 a.a.*

Chain R: Q5SLQ0 (RS18_THET8)

Seq:				88 a.a.

Struc:				73 a.a.*

Chain S: Q5SHP2 (RS19_THET8)

Seq:				93 a.a.

Struc:				84 a.a.

Chain T: P80380 (RS20_THET8)

Seq:				106 a.a.

Struc:				99 a.a.*

Chain V: Q5SIH3 (RSHX_THET8)

Seq:

27 a.a.

Struc:

24 a.a.

Key:		PfamA domain			PfamB domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Resolution:

3.00Å

R-factor:

0.221

R-free:

0.255

Authors:

A.P.Carter,W.M.Clemons Jr.,D.E.Brodersen,B.T.Wimberly, R.J.Morgan-Warren,V.Ramakrishnan

Key ref:

A.P.Carter et al. (2000). Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.. Nature, 407, 340-348. [PubMed id: 11014183] [DOI: 10.1038/35030019]

Date:

08-Aug-00

Release date:

25-Sep-00

Related entries:

1qd7
earlier partial model of the 30s particle
1fjf
native structure of the 30s particle

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Key reference

DOI no: 10.1038/35030019 Nature 407:340-348 (2000)

PubMed id: 11014183

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.

A.P.Carter, W.M.Clemons, D.E.Brodersen, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan.

ABSTRACT

The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.

Selected figure(s)

Figure 4.
Figure 4: Interaction of spectinomycin with the 30S ribosomal subunit. a, Difference Fourier maps showing the binding site of spectinomycin in helix 34. b, Chemical structure of spectinomycin, showing interactions of the various groups with specific residues of 30S. c, The spectinomycin-binding site, showing its location at a pivotal point in the head of the 30S subunit. d, Inset showing spectinomycin in a space-filling model, and the location of its binding site on the 30S. Figure 5.
Figure 5: Interaction of streptomycin with the 30S ribosomal subunit. a, Difference Fourier maps showing the binding site of streptomycin. Mutations in ribosomal protein S12 that confer resistance are shown in red. b, Chemical structure of streptomycin, showing interactions of the various groups with specific residues of the ribosome. c, The streptomycin-binding site, showing its interaction with H27, the 530 loop (H18), H44 and ribosomal protein S12. d, A view of the 30S showing streptomycin in a space-filling model, and the surrounding RNA and protein elements.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 407, 340-348) copyright 2000.

Figures were selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

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.

19906714 S.Nozinovic, B.Fürtig, H.R.Jonker, C.Richter, and H.Schwalbe (2010).
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.

Nucleic Acids Res, 38, 683-694.

PDB code: 2koc

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.

19279186 C.Hsiao, and L.D.Williams (2009).
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.

Nucleic Acids Res, 37, 3134-3142.

19114489 C.Lorenz, and D.Büttner (2009).
Functional characterization of the type III secretion ATPase HrcN from the plant pathogen Xanthomonas campestris pv. vesicatoria.

J Bacteriol, 191, 1414-1428.

19154330 D.Qin, and K.Fredrick (2009).
Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA.

Mol Microbiol, 71, 1239-1249.

19104019 G.Wang, T.Inaoka, S.Okamoto, and K.Ochi (2009).
A novel insertion mutation in Streptomyces coelicolor ribosomal S12 protein results in paromomycin resistance and antibiotic overproduction.

Antimicrob Agents Chemother, 53, 1019-1026.

19386726 H.Vallabhaneni, and P.J.Farabaugh (2009).
Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction.

RNA, 15, 1100-1109.

19585638 I.A.Katsoulis, C.Pyrkotis, A.Papakyriakou, G.Kythreoti, A.L.Zografos, I.Mavridis, V.R.Nahmias, P.Anastasopoulou, and D.Vourloumis (2009).
Unnatural rigid scaffolds targeting the bacterial ribosome.

Chembiochem, 10, 1969-1972.

19137609 J.H.Kim, S.J.Park, K.Y.Lee, W.S.Son, N.Y.Sohn, A.R.Kwon, and B.J.Lee (2009).
Solution structure of hypothetical protein HP1423 (Y1423_HELPY) reveals the presence of alphaL motif related to RNA binding.

Proteins, 75, 252-257.

PDB code: 2k6p

19907650 J.M.Struble, and R.T.Gill (2009).
Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa.

PLoS One, 4, e6576.

19140156 J.Mo, G.C.Todd, and K.Håkansson (2009).
Characterization of nucleic acid higher order structure by gas-phase H/D exchange in a quadrupole-FT-ICR mass spectrometer.

Biopolymers, 91, 256-264.

19429619 P.G.Young, R.Walanj, V.Lakshmi, L.J.Byrnes, P.Metcalf, E.N.Baker, S.B.Vakulenko, and C.A.Smith (2009).
The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] provide insights into substrate selectivity in the APH(2'') subfamily.

J Bacteriol, 191, 4133-4143.

PDB codes: 3ham 3hav

19144908 S.T.Gregory, and A.E.Dahlberg (2009).
Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA.

RNA, 15, 215-223.

19095621 S.T.Gregory, J.F.Carr, and A.E.Dahlberg (2009).
A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA.

RNA, 15, 208-214.

19329536 T.J.Tavares, A.V.Beribisky, and P.E.Johnson (2009).
Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin.

RNA, 15, 911-922.

PDB code: 2rpt

19039528 W.R.Hong, M.Ge, Z.H.Zeng, L.Zhu, M.Y.Luo, L.Shao, and D.J.Chen (2009).
Molecular cloning and sequence analysis of the sisomicin biosynthetic gene cluster from Micromonospora inyoensis.

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18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
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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.

18060665 C.Foster, and W.S.Champney (2008).
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Arch Microbiol, 189, 441-449.

17966131 C.H.Mak (2008).
RNA conformational sampling. I. Single-nucleotide loop closure.

J Comput Chem, 29, 926-933.

18058790 D.Balenci, F.Bernardi, L.Cellai, N.D'Amelio, E.Gaggelli, N.Gaggelli, E.Molteni, and G.Valensin (2008).
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Chembiochem, 9, 114-123.

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Guanidinoneomycin B recognition of an HIV-1 RNA helix.

Chembiochem, 9, 93.

PDB code: 2juk

17987316 E.C.Böttger, and B.Springer (2008).
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Eur J Pediatr, 167, 141-148.

18768810 E.Roberts, A.Sethi, J.Montoya, C.R.Woese, and Z.Luthey-Schulten (2008).
Molecular signatures of ribosomal evolution.

Proc Natl Acad Sci U S A, 105, 13953-13958.

18003936 H.Fan-Minogue, and D.M.Bedwell (2008).
Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity.

RNA, 14, 148-157.

18844986 H.Grosjean, C.Gaspin, C.Marck, W.A.Decatur, and V.de Crécy-Lagard (2008).
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BMC Genomics, 9, 470.

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Nucleic Acids Res, 36, 732-741.

18346970 J.Kondo, and E.Westhof (2008).
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.

Nucleic Acids Res, 36, 2654-2666.

PDB codes: 3bnl 3bnn 3bno 3bnp 3bnq 3bnr 3bns 3bnt

18550838 J.W.Park, J.S.Hong, N.Parajuli, W.S.Jung, S.R.Park, S.K.Lim, J.K.Sohng, and Y.J.Yoon (2008).
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Proc Natl Acad Sci U S A, 105, 8399-8404.

18310077 K.Fukui, M.Nishida, N.Nakagawa, R.Masui, and S.Kuramitsu (2008).
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J Biol Chem, 283, 12136-12145.

18485067 L.E.Lancaster, A.Savelsbergh, C.Kleanthous, W.Wintermeyer, and M.V.Rodnina (2008).
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Mol Microbiol, 69, 390-401.

18355231 L.P.Thapa, T.J.Oh, K.Liou, and J.K.Sohng (2008).
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J Appl Microbiol, 105, 300-308.

18567815 M.A.Borovinskaya, S.Shoji, K.Fredrick, and J.H.Cate (2008).
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RNA, 14, 1590-1599.

PDB codes: 3df1 3df2 3df3 3df4

18174989 M.Hainrichson, I.Nudelman, and T.Baasov (2008).
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.

Org Biomol Chem, 6, 227-239.

18187576 M.Simonović, and T.A.Steitz (2008).
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.

Proc Natl Acad Sci U S A, 105, 500-505.

18685777 N.M.Llewellyn, and J.B.Spencer (2008).
Chemoenzymatic acylation of aminoglycoside antibiotics.

Chem Commun (Camb), 0, 3786-3788.

18802637 Q.Fan, F.Huang, P.F.Leadlay, and J.B.Spencer (2008).
The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233: genetic and biochemical evidence for the roles of two glycosyltransferases and a deacetylase.

Org Biomol Chem, 6, 3306-3314.

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.

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.

18927606 R.S.Mathew-Fenn, R.Das, J.A.Silverman, P.A.Walker, and P.A.Harbury (2008).
A molecular ruler for measuring quantitative distance distributions.

PLoS ONE, 3, e3229.

18221556 S.L.Liu, and K.Adams (2008).
Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids.

BMC Evol Biol, 8, 25.

19104050 S.N.Hobbie, S.Akshay, S.K.Kalapala, C.M.Bruell, D.Shcherbakov, and E.C.Böttger (2008).
Genetic analysis of interactions with eukaryotic rRNA identify the mitoribosome as target in aminoglycoside ototoxicity.

Proc Natl Acad Sci U S A, 105, 20888-20893.

18263620 T.Sun, and Y.Zhang (2008).
Pentamidine binds to tRNA through non-specific hydrophobic interactions and inhibits aminoacylation and translation.

Nucleic Acids Res, 36, 1654-1664.

17591769 A.Yassin, and A.S.Mankin (2007).
Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit.

J Biol Chem, 282, 24329-24342.

17848413 B.W.Ying, D.Fourmy, and S.Yoshizawa (2007).
Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA.

RNA, 13, 2042-2050.

17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.

PLoS Comput Biol, 3, e211.

17621298 C.Köhrer, and U.L.RajBhandary (2007).
An evolved ribosome for genetic code expansion.

Nat Biotechnol, 25, 745-746.

17353247 C.M.Barbieri, M.Kaul, M.Bozza-Hingos, F.Zhao, Y.Tor, T.Hermann, and D.S.Pilch (2007).
Defining the molecular forces that determine the impact of neomycin on bacterial protein synthesis: importance of the 2'-amino functionality.

Antimicrob Agents Chemother, 51, 1760-1769.

17416634 C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, and V.Ramakrishnan (2007).
Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.

RNA, 13, 817-823.

PDB codes: 2uxb 2uxc 2uxd

17146803 C.Shammas, J.A.Donarski, and V.Ramesh (2007).
NMR structure of the peptidyl transferase RNA inhibitor antibiotic amicetin.

Magn Reson Chem, 45, 133-141.

17671368 D.Iino, Y.Takakura, M.Kuroiwa, R.Kawakami, Y.Sasaki, T.Hoshino, K.Ohsawa, A.Nakamura, and S.Yajima (2007).
Crystallization and preliminary crystallographic analysis of hygromycin B phosphotransferase from Escherichia coli.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 685-688.

17592040 D.L.Taliaferro, and P.J.Farabaugh (2007).
Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site.

RNA, 13, 1279-1286.

17317625 D.Pan, S.V.Kirillov, and B.S.Cooperman (2007).
Kinetically competent intermediates in the translocation step of protein synthesis.

Mol Cell, 25, 519-529.

17095544 E.B.Kramer, and P.J.Farabaugh (2007).
The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.

RNA, 13, 87-96.

17601820 E.Blas-Galindo, F.Cava, E.López-Viñas, J.Mendieta, and J.Berenguer (2007).
Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus.

Appl Environ Microbiol, 73, 5138-5145.

17565370 E.P.Plant, P.Nguyen, J.R.Russ, Y.R.Pittman, T.Nguyen, J.T.Quesinberry, T.G.Kinzy, and J.D.Dinman (2007).
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.

PLoS ONE, 2, e517.

18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.

Future Microbiol, 2, 571-574.

17650474 G.G.Perron, A.Gonzalez, and A.Buckling (2007).
Source-sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost.

Proc Biol Sci, 274, 2351-2356.

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.

17394637 I.Sermet-Gaudelus, M.Renouil, A.Fajac, L.Bidou, B.Parbaille, S.Pierrot, N.Davy, E.Bismuth, P.Reinert, G.Lenoir, J.F.Lesure, J.P.Rousset, and A.Edelman (2007).
In vitro prediction of stop-codon suppression by intravenous gentamicin in patients with cystic fibrosis: a pilot study.

BMC Med, 5, 5.

17412704 J.Bischerour, and R.Chalmers (2007).
Base-flipping dynamics in a DNA hairpin processing reaction.

Nucleic Acids Res, 35, 2584-2595.

17705310 J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, C.M.Barbieri, D.S.Pilch, E.Westhof, and T.Baasov (2007).
Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.

Chembiochem, 8, 1700-1709.

PDB codes: 2o3v 2o3w 2o3x 2o3y

17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.

Acta Crystallogr D Biol Crystallogr, 63, 673-681.

PDB code: 2got

17384190 J.R.Nodwell (2007).
Novel links between antibiotic resistance and antibiotic production.

J Bacteriol, 189, 3683-3685.

17875999 J.Wachino, K.Shibayama, H.Kurokawa, K.Kimura, K.Yamane, S.Suzuki, N.Shibata, Y.Ike, and Y.Arakawa (2007).
Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides.

Antimicrob Agents Chemother, 51, 4401-4409.

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.

17284856 K.Asai, T.Inaoka, H.Nanamiya, Y.Sadaie, K.Ochi, and F.Kawamura (2007).
Isolation and characterization of sporulation-initiation mutation in the Bacillus subtilis prfB gene.

Biosci Biotechnol Biochem, 71, 397-406.

17573471 K.Nishimura, S.K.Johansen, T.Inaoka, T.Hosaka, S.Tokuyama, Y.Tahara, S.Okamoto, F.Kawamura, S.Douthwaite, and K.Ochi (2007).
Identification of the RsmG methyltransferase target as 16S rRNA nucleotide G527 and characterization of Bacillus subtilis rsmG mutants.

J Bacteriol, 189, 6068-6073.

17384192 K.Nishimura, T.Hosaka, S.Tokuyama, S.Okamoto, and K.Ochi (2007).
Mutations in rsmG, encoding a 16S rRNA methyltransferase, result in low-level streptomycin resistance and antibiotic overproduction in Streptomyces coelicolor A3(2).

J Bacteriol, 189, 3876-3883.

17587668 K.Ochi (2007).
From microbial differentiation to ribosome engineering.

Biosci Biotechnol Biochem, 71, 1373-1386.

17704156 K.Réblová, E.Fadrná, J.Sarzynska, T.Kulinski, P.Kulhánek, E.Ennifar, J.Koca, and J.Sponer (2007).
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.

Biophys J, 93, 3932-3949.

17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.

Proteins, 68, 109-122.

17592474 K.Wang, H.Neumann, S.Y.Peak-Chew, and J.W.Chin (2007).
Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.

Nat Biotechnol, 25, 770-777.

17159993 L.Cochella, J.L.Brunelle, and R.Green (2007).
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.

Nat Struct Mol Biol, 14, 30-36.

17159922 L.L.Silver (2007).
Multi-targeting by monotherapeutic antibacterials.

Nat Rev Drug Discov, 6, 41-55.

17660832 M.A.Borovinskaya, R.D.Pai, W.Zhang, B.S.Schuwirth, J.M.Holton, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2007).
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.

Nat Struct Mol Biol, 14, 727-732.

PDB codes: 2qal 2qam 2qan 2qao 2qb9 2qba 2qbb 2qbc 2qbd 2qbe 2qbf 2qbg 2qbh 2qbi 2qbj 2qbk 2z4k 2z4l 2z4m 2z4n

17394189 M.D.Disney, and J.L.Childs-Disney (2007).
Using selection to identify and chemical microarray to study the RNA internal loops recognized by 6'-N-acylated kanamycin A.

Chembiochem, 8, 649-656.

17210778 M.Goswami, S.H.Mangoli, and N.Jawali (2007).
Effects of glutathione and ascorbic acid on streptomycin sensitivity of Escherichia coli.

Antimicrob Agents Chemother, 51, 1119-1122.

17804668 M.Kaczanowska, and M.Rydén-Aulin (2007).
Ribosome biogenesis and the translation process in Escherichia coli.

Microbiol Mol Biol Rev, 71, 477-494.

17564727 M.O'connor (2007).
Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli.

Mol Genet Genomics, 278, 307-315.

17323326 P.C.Anderson, and S.Mecozzi (2007).
Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site A.

Biopolymers, 86, 95.

17391549 P.C.Bevilacqua, A.L.Cerrone-Szakal, and N.A.Siegfried (2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.

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17399988 P.W.Chao, and C.S.Chow (2007).
Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching.

Bioorg Med Chem, 15, 3825-3831.

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

17766247 S.N.Hobbie, S.K.Kalapala, S.Akshay, C.Bruell, S.Schmidt, S.Dabow, A.Vasella, P.Sander, and E.C.Böttger (2007).
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17539821 S.O.Meroueh, and S.Mobashery (2007).
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17238915 S.Okamoto, A.Tamaru, C.Nakajima, K.Nishimura, Y.Tanaka, S.Tokuyama, Y.Suzuki, and K.Ochi (2007).
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Mol Microbiol, 63, 1096-1106.

17188860 Y.Zhou, V.E.Gregor, B.K.Ayida, G.C.Winters, Z.Sun, D.Murphy, G.Haley, D.Bailey, J.M.Froelich, S.Fish, S.E.Webber, T.Hermann, and D.Wall (2007).
Synthesis and SAR of 3,5-diamino-piperidine derivatives: novel antibacterial translation inhibitors as aminoglycoside mimetics.

Bioorg Med Chem Lett, 17, 1206-1210.

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.

16721598 A.W.Strittmatter, C.Fischer, M.Kleinschmidt, and G.H.Braus (2006).
FLO11 mediated filamentous growth of the yeast Saccharomyces cerevisiae depends on the expression of the ribosomal RPS26 genes.

Mol Genet Genomics, 276, 113-125.

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.

16998486 B.S.Schuwirth, J.M.Day, C.W.Hau, G.R.Janssen, A.E.Dahlberg, J.H.Cate, and A.Vila-Sanjurjo (2006).
Structural analysis of kasugamycin inhibition of translation.

Nat Struct Mol Biol, 13, 879-886.

PDB codes: 1vs5 1vs6 1vs7 1vs8

17129165 C.Hyeon, R.I.Dima, and D.Thirumalai (2006).
Size, shape, and flexibility of RNA structures.

J Chem Phys, 125, 194905.

16390446 D.Büttner, C.Lorenz, E.Weber, and U.Bonas (2006).
Targeting of two effector protein classes to the type III secretion system by a HpaC- and HpaB-dependent protein complex from Xanthomonas campestris pv. vesicatoria.

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16436695 D.Criswell, V.L.Tobiason, J.S.Lodmell, and D.S.Samuels (2006).
Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi.

Antimicrob Agents Chemother, 50, 445-452.

16957210 D.Dailidiene, G.Dailide, D.Kersulyte, and D.E.Berg (2006).
Contraselectable streptomycin susceptibility determinant for genetic manipulation and analysis of Helicobacter pylori.

Appl Environ Microbiol, 72, 5908-5914.

16679451 E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.M.Weibel, A.M.Aubertin, P.Pale, P.Dumas, and R.Marquet (2006).
Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell.

Nucleic Acids Res, 34, 2328-2339.

PDB codes: 2fcx 2fcy 2fcz 2fd0

17381338 E.M.Youngman, L.Cochella, J.L.Brunelle, S.He, and R.Green (2006).
Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors.

Cold Spring Harb Symp Quant Biol, 71, 545-549.

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

16881035 F.von Nussbaum, M.Brands, B.Hinzen, S.Weigand, and D.Häbich (2006).
Antibacterial natural products in medicinal chemistry--exodus or revival?

Angew Chem Int Ed Engl, 45, 5072-5129.

16717405 H.Yoneyama, and R.Katsumata (2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.

Biosci Biotechnol Biochem, 70, 1060-1075.

16724458 J.Donarski, C.Shammas, R.Banks, and V.Ramesh (2006).
NMR and molecular modelling studies of the binding of amicetin antibiotic to conserved secondary structural motifs of 23S ribosomal RNAs.

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16484214 J.F.Carr, D.M.Hamburg, S.T.Gregory, P.A.Limbach, and A.E.Dahlberg (2006).
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J Bacteriol, 188, 2020-2023.

16452297 J.Kondo, A.Urzhumtsev, and E.Westhof (2006).
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.

Nucleic Acids Res, 34, 676-685.

PDB code: 2fqn

16596680 J.Kondo, B.François, A.Urzhumtsev, and E.Westhof (2006).
Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin.

Angew Chem Int Ed Engl, 45, 3310-3314.

PDB code: 2g5k

16489185 J.S.Feinberg, and S.Joseph (2006).
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RNA, 12, 580-588.

16485038 K.Hamacher, J.Trylska, and J.A.McCammon (2006).
Dependency map of proteins in the small ribosomal subunit.

PLoS Comput Biol, 2, e10.

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.

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16391027 K.Kurosawa, T.Hosaka, N.Tamehiro, T.Inaoka, and K.Ochi (2006).
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Appl Environ Microbiol, 72, 71-77.

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.

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.

16565414 L.D.Kapp, S.E.Kolitz, and J.R.Lorsch (2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.

RNA, 12, 751-764.

16408312 M.Kaiser, M.Sainlos, J.M.Lehn, S.Bombard, and M.P.Teulade-Fichou (2006).
Aminoglycoside-quinacridine conjugates: towards recognition of the P6.1 element of telomerase RNA.

Chembiochem, 7, 321-329.

16500956 M.Newby Lambert, E.Vöcker, S.Blumberg, S.Redemann, A.Gajraj, J.C.Meiners, and N.G.Walter (2006).
Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.

Biophys J, 90, 3672-3685.

16959973 M.Selmer, C.M.Dunham, F.V.Murphy, A.Weixlbaumer, S.Petry, A.C.Kelley, J.R.Weir, and V.Ramakrishnan (2006).
Structure of the 70S ribosome complexed with mRNA and tRNA.

Science, 313, 1935-1942.

PDB codes: 2j00 2j01 2j02 2j03

17012271 N.E.McCrate, M.E.Varner, K.I.Kim, and M.C.Nagan (2006).
Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.

Nucleic Acids Res, 34, 5361-5368.

17053085 N.Kirthi, B.Roy-Chaudhuri, T.Kelley, and G.M.Culver (2006).
A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity.

RNA, 12, 2080-2091.

17119636 N.M.Llewellyn, and J.B.Spencer (2006).
Biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.

Nat Prod Rep, 23, 864-874.

17016423 P.Imming, C.Sinning, and A.Meyer (2006).
Drugs, their targets and the nature and number of drug targets.

Nat Rev Drug Discov, 5, 821-834.

17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.

Mol Cell Biol, 26, 8992-9002.

16679452 S.Lemieux, and F.Major (2006).
Automated extraction and classification of RNA tertiary structure cyclic motifs.

Nucleic Acids Res, 34, 2340-2346.

16569869 S.N.Hobbie, P.Pfister, C.Bruell, P.Sander, B.François, E.Westhof, and E.C.Böttger (2006).
Binding of neomycin-class aminoglycoside antibiotics to mutant ribosomes with alterations in the A site of 16S rRNA.

Antimicrob Agents Chemother, 50, 1489-1496.

16859496 T.Hosaka, J.Xu, and K.Ochi (2006).
Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant.

Mol Microbiol, 61, 883-897.

16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.

Mol Microbiol, 59, 1664-1677.

17038497 V.Berk, W.Zhang, R.D.Pai, J.H.Cate, and J.H.Cate (2006).
Structural basis for mRNA and tRNA positioning on the ribosome.

Proc Natl Acad Sci U S A, 103, 15830-15834.

PDB codes: 2i2p 2i2t 2i2u 2i2v

16557321 Y.Rao, A.Venot, E.E.Swayze, R.H.Griffey, and G.J.Boons (2006).
Trisaccharide mimetics of the aminoglycoside antibiotic neomycin.

Org Biomol Chem, 4, 1328-1337.

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.

16214802 B.François, R.J.Russell, J.B.Murray, F.Aboul-ela, B.Masquida, Q.Vicens, and E.Westhof (2005).
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.

Nucleic Acids Res, 33, 5677-5690.

PDB codes: 2esi 2esj 2et3 2et4 2et5 2et8

15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.

FEBS J, 272, 2098-2108.

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.

15872184 F.Bélanger, G.Théberge-Julien, P.R.Cunningham, and L.Brakier-Gingras (2005).
A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome.

RNA, 11, 906-913.

15984036 F.Corzana, I.Cuesta, A.Bastida, A.Hidalgo, M.Latorre, C.González, E.García-Junceda, J.Jiménez-Barbero, and J.L.Asensio (2005).
Molecular recognition of aminoglycoside antibiotics by bacterial defence proteins: NMR study of the structural and conformational features of streptomycin inactivation by Bacillus subtilis aminoglycoside-6-adenyl transferase.

Chemistry, 11, 5102-5113.

16037995 F.Zhao, Q.Zhao, K.F.Blount, Q.Han, Y.Tor, and T.Hermann (2005).
Molecular recognition of RNA by neomycin and a restricted neomycin derivative.

Angew Chem Int Ed Engl, 44, 5329-5334.

PDB codes: 1zx7 1zz5 2a04

16199759 H.Liang, L.F.Landweber, and J.R.Fresco (2005).
Are stop codons recognized by base triplets in the large ribosomal RNA subunit?

RNA, 11, 1478-1484.

16095538 I.Majumdar, S.S.Krishna, and N.V.Grishin (2005).
PALSSE: a program to delineate linear secondary structural elements from protein structures.

BMC Bioinformatics, 6, 202.

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.

15866943 J.F.Carr, S.T.Gregory, and A.E.Dahlberg (2005).
Severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein S12 of Thermus thermophilus depends on the identity of highly conserved amino acid residues.

J Bacteriol, 187, 3548-3550.

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.

15756640 J.Sandbrink, D.Ossipov, H.Aström, and R.Strömberg (2005).
Investigation of potential RNA bulge stabilizing elements.

J Mol Recognit, 18, 318-326.

15855514 J.T.Lin, M.B.Connelly, C.Amolo, S.Otani, and D.S.Yaver (2005).
Global transcriptional response of Bacillus subtilis to treatment with subinhibitory concentrations of antibiotics that inhibit protein synthesis.

Antimicrob Agents Chemother, 49, 1915-1926.