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PDBsum entry 2qb9
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2qb9

 

 

 

 

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Contents
Protein chains
206 a.a. *
205 a.a. *
150 a.a. *
100 a.a. *
150 a.a. *
129 a.a. *
127 a.a. *
98 a.a. *
117 a.a. *
123 a.a. *
114 a.a. *
96 a.a. *
88 a.a. *
82 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
218 a.a. *
51 a.a. *
DNA/RNA
Ligands
LLL ×3
Metals
_MG ×60
Waters ×300
* Residue conservation analysis
Obsolete entry
PDB id:
2qb9
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin. This file contains the 30s subunit of the first 70s ribosome, with gentamicin bound. The entire crystal structure contains two 70s ribosomes and is described in remark 400.
Structure: 16s rrna. Chain: a. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5. Chain: e. 30s ribosomal protein s6.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Resolution:
3.54Å     R-factor:   0.281     R-free:   0.320
Authors: M.A.Borovinskaya,R.D.Pai,W.Zhang,B.-S.Schuwirth,J.M.Holton, G.Hirokawa,H.Kaji,A.Kaji,J.H.D.Cate
Key ref:
M.A.Borovinskaya et al. (2007). Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Biol, 14, 727-732. PubMed id: 17660832 DOI: 10.1038/nsmb1271
Date:
16-Jun-07     Release date:   25-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3 from Escherichia coli (strain K12)
Seq:
Struc: 		233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4 from Escherichia coli (strain K12)
Seq:
Struc: 		206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5 from Escherichia coli (strain K12)
Seq:
Struc: 		167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P02358  (RS6_ECOLI) -  30S ribosomal protein S6 from Escherichia coli (strain K12)
Seq:
Struc: 		135 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8 from Escherichia coli (strain K12)
Seq:
Struc: 		130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9 from Escherichia coli (strain K12)
Seq:
Struc: 		130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10 from Escherichia coli (strain K12)
Seq:
Struc: 		103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11 from Escherichia coli (strain K12)
Seq:
Struc: 		129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12 from Escherichia coli (strain K12)
Seq:
Struc: 		124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14 from Escherichia coli (strain K12)
Seq:
Struc: 		101 a.a.
96 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ4  (RS15_ECOLI) -  30S ribosomal protein S15 from Escherichia coli (strain K12)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16 from Escherichia coli (strain K12)
Seq:
Struc: 		82 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17 from Escherichia coli (strain K12)
Seq:
Struc: 		84 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18 from Escherichia coli (strain K12)
Seq:
Struc: 		75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19 from Escherichia coli (strain K12)
Seq:
Struc: 		92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20 from Escherichia coli (strain K12)
Seq:
Struc: 		87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2 from Escherichia coli (strain K12)
Seq:
Struc: 		241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
P68679  (RS21_ECOLI) -  30S ribosomal protein S21 from Escherichia coli (strain K12)
Seq:
Struc: 		71 a.a.
51 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chain
  U-G-A-A-G-A-G-U-U-U-G-A-U-C-A-U-G-G-C-U-C-A-G-A-U-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1530 bases

 

 
DOI no: 10.1038/nsmb1271 Nat Struct Biol 14:727-732 (2007)
PubMed id: 17660832  
 
 
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
M.A.Borovinskaya, R.D.Pai, W.Zhang, B.S.Schuwirth, J.M.Holton, G.Hirokawa, H.Kaji, A.Kaji, J.H.Cate.
 
  ABSTRACT  
 
Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.
 
  Selected figure(s)  
 
Figure 1.
(a) Chemical structures of neomycin, paromomycin and gentamicin. (b) Global view of the ribosome and the two binding sites for aminoglycosides. Gold and green, aminoglycosides bound to the 30S and 50S subunits, respectively; light blue, 16S rRNA; gray, 23S rRNA; purple, 5S rRNA; dark blue and magenta, proteins of small and large subunits, respectively; CP, central protuberance. (c) Close-up view of the two binding sites in h44 and H69, shown with neomycin as an example. Neomycin molecules bound to h44 and H69 are in gold and green, respectively. Green, orange and blue shadows outline positions that would be occupied by mRNA, A-site tRNA and P-site tRNA, respectively. The mRNA and tRNAs are above the plane of the image. Inset shows direction of view. 		Figure 3.
(a) F[o] – F[o] difference electron density map, truncated at 6-Šresolution, comparing 70S ribosome crystals in complex with RRF to ribosomes in complex with neomycin. In the absence of RRF, the overall position of H69 at the interface in apo–70S ribosomes is essentially identical to that in neomycin-bound ribosomes (Supplementary Methods). Only domain I of RRF is visible; domain II is located to the right of the view shown. Blue, positive difference density; red, negative difference density; arrow, direction of the conformational change in H69 upon RRF binding. (b) F[o] – F[o] difference electron density as in a, but at 3.5-Šresolution. Insets in a and b show angles of view.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2007, 14, 727-732) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
21323758 Y.Zhang, and M.Inouye (2011).
RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation.
  Mol Microbiol, 79, 1418-1429.  
20110260 A.E.Scheunemann, W.D.Graham, F.A.Vendeix, and P.F.Agris (2010).
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.
  Nucleic Acids Res, 38, 3094-3105.  
20385807 D.B.Johnson, and L.Wang (2010).
Imprints of the genetic code in the ribosome.
  Proc Natl Acad Sci U S A, 107, 8298-8303.  
20668033 D.E.Burakovsky, P.V.Sergiev, M.A.Steblyanko, A.V.Kubarenko, A.L.Konevega, A.A.Bogdanov, M.V.Rodnina, and O.A.Dontsova (2010).
Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination.
  RNA, 16, 1848-1853.  
20651030 E.B.Kramer, H.Vallabhaneni, L.M.Mayer, and P.J.Farabaugh (2010).
A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae.
  RNA, 16, 1797-1808.  
20525206 F.Babić, V.Venturi, and G.Maravić-Vlahovicek (2010).
Tobramycin at subinhibitory concentration inhibits the RhlI/R quorum sensing system in a Pseudomonas aeruginosa environmental isolate.
  BMC Infect Dis, 10, 148.  
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.  
19946275 M.B.Feldman, D.S.Terry, R.B.Altman, and S.C.Blanchard (2010).
Aminoglycoside activity observed on single pre-translocation ribosome complexes.
  Nat Chem Biol, 6, 54-62.  
20629012 P.B.Tsitovich, A.Pushechnikov, J.M.French, and M.D.Disney (2010).
A chemoenzymatic route to diversify aminoglycosides enables a microarray-based method to probe acetyltransferase activity.
  Chembiochem, 11, 1656-1660.  
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
20108982 T.Tran, and M.D.Disney (2010).
Two-dimensional combinatorial screening of a bacterial rRNA A-site-like motif library: defining privileged asymmetric internal loops that bind aminoglycosides.
  Biochemistry, 49, 1833-1842.  
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.  
19324963 A.Savelsbergh, M.V.Rodnina, and W.Wintermeyer (2009).
Distinct functions of elongation factor G in ribosome recycling and translocation.
  RNA, 15, 772-780.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19258531 B.A.Maguire (2009).
Inhibition of bacterial ribosome assembly: a suitable drug target?
  Microbiol Mol Biol Rev, 73, 22-35.  
19726586 D.J.Paul, S.J.Seedhouse, and M.D.Disney (2009).
Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions.
  Nucleic Acids Res, 37, 5894-5907.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19776006 L.E.Holberger, and C.S.Hayes (2009).
Ribosomal protein S12 and aminoglycoside antibiotics modulate A-site mRNA cleavage and transfer-messenger RNA activity in Escherichia coli.
  J Biol Chem, 284, 32188-32200.  
19324965 M.A.Zundel, G.N.Basturea, and M.P.Deutscher (2009).
Initiation of ribosome degradation during starvation in Escherichia coli.
  RNA, 15, 977-983.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
19589804 M.Savic, J.Lovric, T.I.Tomic, B.Vasiljevic, and G.L.Conn (2009).
Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics.
  Nucleic Acids Res, 37, 5420-5431.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19501253 X.G.Zhang, P.W.Mason, E.J.Dubovi, X.Xu, N.Bourne, R.W.Renshaw, T.M.Block, and A.V.Birk (2009).
Antiviral activity of geneticin against dengue virus.
  Antiviral Res, 83, 21-27.  
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
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.  
18948280 G.Hirokawa, N.Iwakura, A.Kaji, and H.Kaji (2008).
The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G).
  Nucleic Acids Res, 36, 6676-6687.  
18931791 J.P.Desaulniers, Y.C.Chang, R.Aduri, S.C.Abeysirigunawardena, J.SantaLucia, and C.S.Chow (2008).
Pseudouridines in rRNA helix 69 play a role in loop stacking interactions.
  Org Biomol Chem, 6, 3892-3895.  
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
18685777 N.M.Llewellyn, and J.B.Spencer (2008).
Chemoenzymatic acylation of aminoglycoside antibiotics.
  Chem Commun (Camb), (), 3786-3788.  
18234219 R.D.Pai, W.Zhang, B.S.Schuwirth, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2008).
Structural Insights into ribosome recycling factor interactions with the 70S ribosome.
  J Mol Biol, 376, 1334-1347.  
18268024 S.C.Abeysirigunawardena, and C.S.Chow (2008).
pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
  RNA, 14, 782-792.  
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
17967466 D.Sharma, A.R.Cukras, E.J.Rogers, D.R.Southworth, and R.Green (2007).
Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome.
  J Mol Biol, 374, 1065-1076.  
18042450 E.M.Youngman, S.L.He, L.J.Nikstad, and R.Green (2007).
Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release.
  Mol Cell, 28, 533-543.  
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.  
17996252 N.Gao, A.V.Zavialov, M.Ehrenberg, and J.Frank (2007).
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
  J Mol Biol, 374, 1345-1358.
PDB code: 2rdo
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.

 

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