PDBsum entry: 1ibk

Ribosome

PDB-id

1ibk


	Asymmetric unit

	Main view

Contents

Description

Header details

Protein chains

DNA/RNA

Ligands

PAR

Metal ions

_MG ×113

_ZN ×2

* Residue conservation analysis

Tools

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Clefts Calculation

		Biological unit, 22mer (as deduced by PQS)

PDB id:

1ibk

Name:

Ribosome

Title:

Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotic paromomycin

Structure:

16s ribosomal RNA. Chain: a. P-site messenger RNA fragment. 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:				234 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:				124 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:				80 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 3 residue positions (black crosses)

Resolution:

3.31Å

R-factor:

0.229

R-free:

0.282

Authors:

J.M.Ogle,D.E.Brodersen,W.M.Clemons Jr.,M.J.Tarry,A.P.Carter, V.Ramakrishnan

Key ref:

J.M.Ogle et al. (2001). Recognition of cognate transfer RNA by the 30S ribosomal subunit.. Science, 292, 897-902. [PubMed id: 11340196] [DOI: 10.1126/science.1060612]

Date:

28-Mar-01

Release date:

04-May-01

Related entries:

1fjf
native structure of the 30s particle
1fjg
structure of the 30s particle in complex with the
antibiotics streptomycin, spectinomycin and paromomycin
1ibl
structure of the 30s particle in complex with messenger RNA
fragment and cognate transfer RNA anticodon stem-loop bound
to the a site and with the antibiotic paromomycin
1ibm
... plus others (see Header records)

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Key reference

DOI no: 10.1126/science.1060612 Science 292:897-902 (2001)

PubMed id: 11340196

Recognition of cognate transfer RNA by the 30S ribosomal subunit.

J.M.Ogle, D.E.Brodersen, W.M.Clemons, M.J.Tarry, A.P.Carter, V.Ramakrishnan.

ABSTRACT

Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.

Selected figure(s)

Figure 2.
Fig. 2. Complex of the 30S subunit with mRNA from a U[6] hexanucleotide and a cognate tRNA-ASL. (A) Overview of the complex. The 50S interface side of the 30S subunit is facing the reader, and important elements have been given standard colors that are used throughout the figures, namely, ASL at the A site (gold), codon from the U[6] hexanucleotide at the A site (purple), 3' end of 16S RNA that mimics mRNA at the P site (green), P site tRNA mimic introduced by helix 6 from a neighboring molecule (dark blue), and protein S12 (tan). (B) Stereo view showing details of the A and P sites, colored as in (A), with, in addition, helix 44 (cyan, right), helix 34 (blue, left), 530 loop (green, left), and paromomycin (yellow sticks, within helix 44). The hydrogen bonds responsible for the codon-anticodon interaction at both the A and P sites are shown as red lines. Figure 3.
Fig. 3. Stereo views showing interactions of the ribosome with the codon-anticodon base pairs. The tightness of the interactions is shown by the semitransparent van der Waals surface. (A) In the first position, A1493 binds in the minor groove of the A36-U1 base pair. (B) In the second position, G530 and A1492 (both brown) act in concert to monitor the A35-U2 base pair. (C) The third (wobble) position, showing the G34-U3 base pair. C1054 stacks against G36 of the ASL. U3 interacts with G530, and indirectly through a Mg2+ ion (magenta) with C518 and residue Pro48 (E. coli Pro44) from protein S12 (gray). The base pair seems closer to Watson-Crick geometry. (D) The third position in the presence of paromomycin, with the expected GU wobble pair. The interactions with the ribosome are similar to those in (C).

The above figures are reprinted by permission from the AAAs: Science (2001, 292, 897-902) copyright 2001.

Figures were selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

19899089 K.D.Green, W.Chen, J.L.Houghton, M.Fridman, and S.Garneau-Tsodikova (2010).
Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides.

Chembiochem, 11, 119-126.

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.

20005802 C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, and D.E.Brodersen (2009).
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.

Cell, 139, 1084-1095.

PDB codes: 3kha 3kiq 3kir 3kis 3kit 3kiu 3kiw 3kix 3kiy

19019162 E.Diago-Navarro, L.Mora, R.H.Buckingham, R.Díaz-Orejas, and M.Lemonnier (2009).
Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.

Mol Microbiol, 71, 66-78.

19216718 F.Salvatori, V.Cantale, G.Breveglieri, C.Zuccato, A.Finotti, N.Bianchi, M.Borgatti, G.Feriotto, F.Destro, A.Canella, L.Breda, S.Rivella, and R.Gambari (2009).
Development of K562 cell clones expressing beta-globin mRNA carrying the beta039 thalassaemia mutation for the screening of correctors of stop-codon mutations.

Biotechnol Appl Biochem, 54, 41-52.

19343177 G.Zhang, and Z.Ignatova (2009).
Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis.

PLoS ONE, 4, e5036.

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.

19229291 J.C.Schuette, F.V.Murphy, A.C.Kelley, J.R.Weir, J.Giesebrecht, S.R.Connell, J.Loerke, T.Mielke, W.Zhang, P.A.Penczek, V.Ramakrishnan, and C.M.Spahn (2009).
GTPase activation of elongation factor EF-Tu by the ribosome during decoding.

EMBO J, 28, 755-765.

PDB codes: 3fic 3fin

19492048 J.Lehmann, M.Cibils, and A.Libchaber (2009).
Emergence of a code in the polymerization of amino acids along RNA templates.

PLoS One, 4, e5773.

19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.

Nature, 457, 977-980.

19081939 M.J.Belousoff, B.Graham, L.Spiccia, and Y.Tor (2009).
Cleavage of RNA oligonucleotides by aminoglycosides.

Org Biomol Chem, 7, 30-33.

19343072 P.Ramaswamy, and S.A.Woodson (2009).
S16 throws a conformational switch during assembly of 30S 5' domain.

Nat Struct Mol Biol, 16, 438-445.

19343067 P.Schimmel, and M.Guo (2009).
A tipping point for mistranslation and disease.

Nat Struct Mol Biol, 16, 348-349.

19132006 S.Nonin-Lecomte, N.Germain-Amiot, R.Gillet, M.Hallier, L.Ponchon, F.Dardel, and B.Felden (2009).
Ribosome hijacking: a role for small protein B during trans-translation.

EMBO Rep, 10, 160-165.

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.

19129224 T.Dale, R.P.Fahlman, M.Olejniczak, and O.C.Uhlenbeck (2009).
Specificity of the ribosomal A site for aminoacyl-tRNAs.

Nucleic Acids Res, 37, 1202-1210.

19833920 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, Y.G.Gao, F.V.Murphy, J.R.Weir, and V.Ramakrishnan (2009).
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.

Science, 326, 688-694.

PDB codes: 2wrn 2wro 2wrq 2wrr

19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.

Nature, 461, 1234-1242.

20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.

Q Rev Biophys, 42, 159-200.

19064930 A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, and H.F.Noller (2008).
Crystal structure of a translation termination complex formed with release factor RF2.

Proc Natl Acad Sci U S A, 105, 19684-19689.

PDB codes: 3f1e 3f1f 3f1g 3f1h

18988853 A.Weixlbaumer, H.Jin, C.Neubauer, R.M.Voorhees, S.Petry, A.C.Kelley, and V.Ramakrishnan (2008).
Insights into translational termination from the structure of RF2 bound to the ribosome.

Science, 322, 953-956.

PDB codes: 2jl5 2jl6 2jl7 2jl8 2wh1 2wh2 2wh3 2wh4

18158305 C.Geary, S.Baudrey, and L.Jaeger (2008).
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors.

Nucleic Acids Res, 36, 1138-1152.

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.

18667428 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine.

J Biol Chem, 283, 26548-26556.

PDB codes: 3dmf 3dmg 3dmh

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).
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.

BMC Genomics, 9, 470.

18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.

Biophys J, 95, 5962-5973.

18094117 H.P.Harding, J.G.Lackey, H.C.Hsu, Y.Zhang, J.Deng, R.M.Xu, M.J.Damha, and D.Ron (2008).
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RNA, 14, 225-232.

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Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.

RNA, 14, 2159-2169.

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

18495942 J.Lehmann, and A.Libchaber (2008).
Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon.

RNA, 14, 1264-1269.

18485067 L.E.Lancaster, A.Savelsbergh, C.Kleanthous, W.Wintermeyer, and M.V.Rodnina (2008).
Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes.

Mol Microbiol, 69, 390-401.

18755834 L.Lancaster, N.J.Lambert, E.J.Maklan, L.H.Horan, and H.F.Noller (2008).
The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.

RNA, 14, 1999-2012.

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

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.

18596689 M.Laurberg, H.Asahara, A.Korostelev, J.Zhu, S.Trakhanov, and H.F.Noller (2008).
Structural basis for translation termination on the 70S ribosome.

Nature, 454, 852-857.

PDB codes: 3d5a 3d5b 3d5c 3d5d

18590561 M.R.Miller, D.W.Healey, S.G.Robison, J.D.Dewey, and A.R.Buskirk (2008).
The role of upstream sequences in selecting the reading frame on tmRNA.

BMC Biol, 6, 29.

18586937 M.Savic, T.Ilic-Tomic, R.Macmaster, B.Vasiljevic, and G.L.Conn (2008).
Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm.

J Bacteriol, 190, 5855-5861.

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.

18818369 M.Simonović, and T.A.Steitz (2008).
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.

RNA, 14, 2372-2378.

PDB codes: 3cma 3cme

18552770 P.F.Agris (2008).
Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications.

EMBO Rep, 9, 629-635.

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.

18824686 R.A.Marshall, M.Dorywalska, and J.D.Puglisi (2008).
Irreversible chemical steps control intersubunit dynamics during translation.

Proc Natl Acad Sci U S A, 105, 15364-15369.

18308926 S.N.Hobbie, C.M.Bruell, S.Akshay, S.K.Kalapala, D.Shcherbakov, and E.C.Böttger (2008).
Mitochondrial deafness alleles confer misreading of the genetic code.

Proc Natl Acad Sci U S A, 105, 3244-3249.

19172743 S.R.Connell, M.Topf, Y.Qin, D.N.Wilson, T.Mielke, P.Fucini, K.H.Nierhaus, and C.M.Spahn (2008).
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.

Nat Struct Mol Biol, 15, 910-915.

18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.

Nat Rev Mol Cell Biol, 9, 242-253.

19020518 W.Li, X.Agirrezabala, J.Lei, L.Bouakaz, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, S.Sanyal, M.Ehrenberg, and J.Frank (2008).
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.

EMBO J, 27, 3322-3331.

PDB codes: 3ep2 3eq3 3eq4

19088750 Y.S.Khairulina, M.V.Molotkov, K.N.Bulygin, D.M.Graifer, A.G.Ven'yaminova, L.Y.Frolova, J.Stahl, and G.G.Karpova (2008).
[Protein S3 Fragments Neighboring mRNA during Elongation and Translation Termination on the Human Ribosome.]

Bioorg Khim, 34, 773-780.

17956616 A.S.Novozhilov, Y.I.Wolf, and E.V.Koonin (2007).
Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.

Biol Direct, 2, 24.

17496902 A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.Vendeix, P.F.Agris, and V.Ramakrishnan (2007).
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines.

Nat Struct Mol Biol, 14, 498-502.

PDB codes: 2uu9 2uua 2uub 2uuc

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

17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.

EMBO J, 26, 2421-2431.

PDB codes: 2p8w 2p8x 2p8y 2p8z

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.

17283215 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2007).
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.

RNA, 13, 305-312.

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.

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.

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.

17722211 J.Kondo, K.Pachamuthu, B.François, J.Szychowski, S.Hanessian, and E.Westhof (2007).
Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity.

ChemMedChem, 2, 1631-1638.

PDB code: 2pwt

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

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.

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.

17923669 L.Desigaux, M.Sainlos, O.Lambert, R.Chevre, E.Letrou-Bonneval, J.P.Vigneron, P.Lehn, J.M.Lehn, and B.Pitard (2007).
Self-assembled lamellar complexes of siRNA with lipidic aminoglycoside derivatives promote efficient siRNA delivery and interference.

Proc Natl Acad Sci U S A, 104, 16534-16539.

17360328 L.H.Horan, and H.F.Noller (2007).
Intersubunit movement is required for ribosomal translocation.

Proc Natl Acad Sci U S A, 104, 4881-4885.

17186006 L.V.Zingman, S.Park, T.M.Olson, A.E.Alekseev, and A.Terzic (2007).
Aminoglycoside-induced translational read-through in disease: overcoming nonsense mutations by pharmacogenetic therapy.

Clin Pharmacol Ther, 81, 99.

17379816 M.E.Saks, and J.S.Conery (2007).
Anticodon-dependent conservation of bacterial tRNA gene sequences.

RNA, 13, 651-660.

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.

17115251 P.Jayaguru, and M.Raghunathan (2007).
Group I intron renders differential susceptibility of Candida albicans to Bleomycin.

Mol Biol Rep, 34, 11-17.

16912867 P.M.McNutt, M.J.Dehart, and L.A.Matej (2007).
Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation.

Plant Cell Rep, 26, 47-60.

17996707 P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, and R.K.Agrawal (2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.

Mol Cell, 28, 434-445.

PDB codes: 2dyj 2r1c 2r1g

17389639 P.V.Sergiev, A.A.Bogdanov, and O.A.Dontsova (2007).
Ribosomal RNA guanine-(N2)-methyltransferases and their targets.

Nucleic Acids Res, 35, 2295-2301.

17921318 S.Chaudhuri, K.Vyas, P.Kapasi, A.A.Komar, J.D.Dinman, S.Barik, and B.Mazumder (2007).
Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation.

RNA, 13, 2224-2237.

17942742 S.J.Näsvall, P.Chen, and G.R.Björk (2007).
The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.

RNA, 13, 2151-2164.

17766247 S.N.Hobbie, S.K.Kalapala, S.Akshay, C.Bruell, S.Schmidt, S.Dabow, A.Vasella, P.Sander, and E.C.Böttger (2007).
Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria.

Nucleic Acids Res, 35, 6086-6093.

17539821 S.O.Meroueh, and S.Mobashery (2007).
Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic.

Chem Biol Drug Des, 69, 291-297.

17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.

RNA, 13, 549-554.

17699629 T.H.Lee, S.C.Blanchard, H.D.Kim, J.D.Puglisi, and S.Chu (2007).
The role of fluctuations in tRNA selection by the ribosome.

Proc Natl Acad Sci U S A, 104, 13661-13665.

16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.

Acta Crystallogr D Biol Crystallogr, 62, 941-945.

16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.

Nucleic Acids Res, 34, 1326-1341.

16510876 A.V.Pisarev, V.G.Kolupaeva, V.P.Pisareva, W.C.Merrick, C.U.Hellen, and T.V.Pestova (2006).
Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex.

Genes Dev, 20, 624-636.

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.

16891415 F.S.Liang, W.A.Greenberg, J.A.Hammond, J.Hoffmann, S.R.Head, and C.H.Wong (2006).
Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays.

Proc Natl Acad Sci U S A, 103, 12311-12316.

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

17051149 G.Yusupova, L.Jenner, B.Rees, D.Moras, and M.Yusupov (2006).
Structural basis for messenger RNA movement on the ribosome.

Nature, 444, 391-394.

PDB codes: 2hgi 2hgj 2hgp 2hgq 2hgr 2hgu

17069639 J.J.Gillespie, J.S.Johnston, J.J.Cannone, and R.R.Gutell (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.

Insect Mol Biol, 15, 657-686.

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).
Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation.

RNA, 12, 580-588.

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.

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.

16510980 R.Utsunomiya, K.Suto, D.Balasundaresan, A.Fukamizu, P.K.Kumar, and H.Mizuno (2006).
Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.

Acta Crystallogr D Biol Crystallogr, 62, 331-338.

PDB code: 2ao5

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

Mol Microbiol, 59, 1664-1677.

16682558 W.Li, J.Sengupta, B.K.Rath, and J.Frank (2006).
Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations.

RNA, 12, 1240-1253.

PDB code: 2gkz

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

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.

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.

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.

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.

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.

16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
Simulating movement of tRNA into the ribosome during decoding.

Proc Natl Acad Sci U S A, 102, 15854-15859.

15905403 L.Cochella, and R.Green (2005).
An active role for tRNA in decoding beyond codon:anticodon pairing.

Science, 308, 1178-1180.

16228651 M.A.Line (2005).
A hypothetical pathway from the RNA to the DNA world.

Orig Life Evol Biosph, 35, 395-400.

15840820 M.Guillier, F.Allemand, M.Graffe, S.Raibaud, F.Dardel, M.Springer, and C.Chiaruttini (2005).
The N-terminal extension of Escherichia coli ribosomal protein L20 is important for ribosome assembly, but dispensable for translational feedback control.

RNA, 11, 728-738.

16177134 M.Kwapisz, P.Cholbinski, A.K.Hopper, J.P.Rousset, and T.Zoladek (2005).
Rsp5 ubiquitin ligase modulates translation accuracy in yeast Saccharomyces cerevisiae.

RNA, 11, 1710-1718.

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.

16116437 M.Olejniczak, T.Dale, R.P.Fahlman, and O.C.Uhlenbeck (2005).
Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding.

Nat Struct Mol Biol, 12, 788-793.

16004388 N.A.Demeshkina, V.A.Stiazhkina, K.N.Bulygin, M.N.Repkova, A.G.Ven'iaminova, and G.G.Karpova (2005).
[Template location on the human ribosome: environment of the mRNA nucleotide adjacent to the A-site codon on the 3'-side]

Bioorg Khim, 31, 295-302.

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.

15849690 Q.Han, Q.Zhao, S.Fish, K.B.Simonsen, D.Vourloumis, J.M.Froelich, D.Wall, and T.Hermann (2005).
Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.

Angew Chem Int Ed Engl, 44, 2694-2700.

PDB code: 1yrj

16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.

Nature, 436, 979-984.

PDB codes: 1zm2 1zm3 1zm4 1zm9

16043501 S.Q.Gu, J.Jöckel, P.Beinker, J.Warnecke, Y.P.Semenkov, M.V.Rodnina, and W.Wintermeyer (2005).
Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit.

RNA, 11, 1374-1384.

15699355 T.R.Sundermeier, D.P.Dulebohn, H.J.Cho, and A.W.Karzai (2005).
A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation.

Proc Natl Acad Sci U S A, 102, 2316-2321.

14681588 A.L.Konevega, N.G.Soboleva, V.I.Makhno, Y.P.Semenkov, W.Wintermeyer, M.V.Rodnina, and V.I.Katunin (2004).
Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions.

RNA, 10, 90.

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

15208366 D.Graifer, M.Molotkov, V.Styazhkina, N.Demeshkina, K.Bulygin, A.Eremina, A.Ivanov, E.Laletina, A.Ven'yaminova, and G.Karpova (2004).
Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites.

Nucleic Acids Res, 32, 3282-3293.

15523473 D.N.Wilson, and K.H.Nierhaus (2004).
The how and Y of cold shock.

Nat Struct Mol Biol, 11, 1026-1028.

14681582 D.Rodriguez-Correa, and A.E.Dahlberg (2004).
Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model.

RNA, 10, 28-33.

15558050 F.V.Murphy, and V.Ramakrishnan (2004).
Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

Nat Struct Mol Biol, 11, 1251-1252.

PDB codes: 1xnq 1xnr

15558052 F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, and P.F.Agris (2004).
The role of modifications in codon discrimination by tRNA(Lys)UUU.

Nat Struct Mol Biol, 11, 1186-1191.

PDB codes: 1xmo 1xmq

15547132 H.F.Noller (2004).
The driving force for molecular evolution of translation.

RNA, 10, 1833-1837.

15004548 K.B.Gromadski, and M.V.Rodnina (2004).
Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome.

Nat Struct Mol Biol, 11, 316-322.

15578054 L.Cochella, and R.Green (2004).
Wobble during decoding: more than third-position promiscuity.

Nat Struct Mol Biol, 11, 1160-1162.

15189156 L.D.Kapp, and J.R.Lorsch (2004).
The molecular mechanics of eukaryotic translation.

Annu Rev Biochem, 73, 657-704.

15608296 L.M.Wadley, and A.M.Pyle (2004).
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery.

Nucleic Acids Res, 32, 6650-6659.

15100436 M.J.Trimble, A.Minnicus, and K.P.Williams (2004).
tRNA slippage at the tmRNA resume codon.

RNA, 10, 805-812.

15247429 M.Léger, S.Sidani, and L.Brakier-Gingras (2004).
A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1.

RNA, 10, 1225-1235.

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.

15509870 M.O'Connor, S.T.Gregory, and A.E.Dahlberg (2004).
Multiple defects in translation associated with altered ribosomal protein L4.

Nucleic Acids Res, 32, 5750-5756.

15009191 N.Chumpolkulwong, C.Hori-Takemoto, T.Hosaka, T.Inaoka, T.Kigawa, M.Shirouzu, K.Ochi, and S.Yokoyama (2004).
Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis.

Eur J Biochem, 271, 1127-1134.

15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.

Nucleic Acids Res, 32, 2342-2352.

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.

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.

15598826 W.Huggins, and P.Wollenzien (2004).
A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome.

Nucleic Acids Res, 32, 6548-6556.

15112238 W.P.Tate, and E.S.Poole (2004).
The ribosome: lifting the veil from a fascinating organelle