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PDBsum entry 1vs5
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1vs5

 

 

 

 

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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
KSG
Metals
_MG ×60
Waters ×300
* Residue conservation analysis
Obsolete entry
PDB id:
1vs5
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. This file contains the 30s subunit of one 70s ribosome. The entire crystal structure contains two 70s ribosomes and is described in remark 400.
Structure: 16s ribosomal RNA. 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
Biol. unit: 21mer (from PQS)
Resolution:
3.46Å     R-factor:   0.279     R-free:   0.331
Authors: B.S.Schuwirth,A.Vila-Sanjurjo,J.H.D.Cate
Key ref:
B.S.Schuwirth et al. (2006). Structural analysis of kasugamycin inhibition of translation. Nat Struct Mol Biol, 13, 879-886. PubMed id: 16998486 DOI: 10.1038/nsmb1150
Date:
04-Aug-06     Release date:   26-Sep-06    
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 ?
Q8X9M2  (RS15_ECO57) -  30S ribosomal protein S15 from Escherichia coli O157:H7
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/nsmb1150 Nat Struct Mol Biol 13:879-886 (2006)
PubMed id: 16998486  
 
 
Structural analysis of kasugamycin inhibition of translation.
B.S.Schuwirth, J.M.Day, C.W.Hau, G.R.Janssen, A.E.Dahlberg, J.H.Cate, A.Vila-Sanjurjo.
 
  ABSTRACT  
 
The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites).
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Determinants of resistance to Ksg in the DASL. (a) Location of the DASL relative to Ksg. DASL residues A1518 and A1519 are shown (gold). Also shown are A792 and G1497 (gray), Ksg (cyan) and distances from the DASL to these residues (in Angstroms). (b) Post-transcriptional modification of the DASL. Plasmid-encoded 16S rRNAs carrying mutations in the DASL (or wild-type (WT) rRNAs) were isolated from ksgA^+ (lanes 3, 7, 11, 15, 19 and 23) or ksgA^- strains (lanes 4, 8, 12, 16, 20 and 24). The presence of the methyl groups at A1518 and/or A1519 in 16S rRNA is detected as a strong reverse-transcriptase stop in primer extension^19. Sequencing lanes, containing rRNA isolated from the ksgA^- strain, are included for every mutant. 		Figure 3.
Figure 3. Chemical modification of mutant and wild-type 30S subunits in the presence of Ksg. Sequencing lanes are labeled U, G, C and A. (a) Ksg footprint in the 794 region of the 16S rRNA upon chemical modification with DMS. (b) Ksg footprint in the 926 region of the 16S rRNA upon chemical modification with kethoxal. The A794G mutation renders the DMS reactivity of this base undetectable, and the G926A mutation makes this residue unreactive to chemical attack by kethoxal; thus, Ksg binding to ribosomes carrying a mutation at one residue was detected as protection of the other residue. Ksg was used at 0, 64 and 320 g ml^-1 (triangles denote increasing concentration). WT, wild-type rRNA.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 879-886) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21242088 W.V.Gilbert (2011).
Functional specialization of ribosomes?
  Trends Biochem Sci, 36, 127-132.  
20034956 A.A.Malygin, and G.G.Karpova (2010).
Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively.
  Nucleic Acids Res, 38, 2089-2098.  
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.  
20544974 Y.Nishida, H.Ishikawa, S.Baba, N.Nakagawa, S.Kuramitsu, and R.Masui (2010).
Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
  Proteins, 78, 2395-2398.
PDB codes: 3af5 3af6
19187763 A.C.Kaberdina, W.Szaflarski, K.H.Nierhaus, and I.Moll (2009).
An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?
  Mol Cell, 33, 227-236.  
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.  
19794129 H.A.Irier, Y.Quan, J.Yoo, and R.Dingledine (2009).
Control of glutamate receptor 2 (GluR2) translational initiation by its alternative 3' untranslated regions.
  Mol Pharmacol, 76, 1145-1149.  
19285505 H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, and G.Jogl (2009).
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
  J Mol Biol, 388, 271-282.
PDB codes: 3fut 3fuu 3fuv 3fuw 3fux
19097863 P.M.Duffin, and H.S.Seifert (2009).
ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.
  Int J Antimicrob Agents, 33, 321-327.  
20043826 R.Binet, and A.T.Maurelli (2009).
The chlamydial functional homolog of KsgA confers kasugamycin sensitivity to Chlamydia trachomatis and impacts bacterial fitness.
  BMC Microbiol, 9, 279.  
19150407 W.K.Olson, M.Esguerra, Y.Xin, and X.J.Lu (2009).
New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures.
  Methods, 47, 177-186.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
17683199 A.L.Manuell, J.Quispe, and S.P.Mayfield (2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
  PLoS Biol, 5, e209.  
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.  
  17894445 C.S.Chow, T.N.Lamichhane, and S.K.Mahto (2007).
Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications.
  ACS Chem Biol, 2, 610-619.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
18033580 N.Dixon, L.S.Wong, T.H.Geerlings, and J.Micklefield (2007).
Cellular targets of natural products.
  Nat Prod Rep, 24, 1288-1310.  
17021617 A.Mankin (2006).
Antibiotic blocks mRNA path on the ribosome.
  Nat Struct Mol Biol, 13, 858-860.  
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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