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PDBsum entry 2qoy

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2qoy
Jmol
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. *
82 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
218 a.a. *
51 a.a. *
88 a.a. *
96 a.a. *
DNA/RNA
Ligands
NMY
SCM
Metals
_MG ×60
Waters ×300
* Residue conservation analysis
PDB id:
2qoy
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin and neomycin. This file contains the 30s subunit of the first 70s ribosome, with spectinomycin and neomycin bound. The entire crystal structure contains two 70s ribosomes.
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:
3.50Å     R-factor:   0.264     R-free:   0.306
Authors: M.A.Borovinskaya,S.Shoji,J.M.Holton,K.Fredrick,J.H.D.Cate
Key ref: M.A.Borovinskaya et al. (2007). A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol, 2, 545-552. PubMed id: 17696316 DOI: 10.1021/cb700100n
Date:
21-Jul-07     Release date:   14-Aug-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q57J38  (RS3_SALCH) -  30S ribosomal protein S3
Seq:
Struc:
233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5
Seq:
Struc:
167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P0A4D2  (RS6_SHIFL) -  30S ribosomal protein S6
Seq:
Struc:
131 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7
Seq:
Struc:
179 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q1R622  (RS8_ECOUT) -  30S ribosomal protein S8
Seq:
Struc:
130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9
Seq:
Struc:
130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10
Seq:
Struc:
103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12
Seq:
Struc:
124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13
Seq:
Struc:
118 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16
Seq:
Struc:
82 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17
Seq:
Struc:
84 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U1  (RS18_SALTI) -  30S ribosomal protein S18
Seq:
Struc:
75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19
Seq:
Struc:
92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20
Seq:
Struc:
87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2
Seq:
Struc:
241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
Q6D9D4  (RS21_ERWCT) -  30S ribosomal protein S21
Seq:
Struc:
71 a.a.
51 a.a.
Protein chain
Pfam   ArchSchema ?
A8A4Y1  (RS15_ECOHS) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14
Seq:
Struc:
101 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   6 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   17 terms 
  Biochemical function     structural constituent of ribosome     18 terms  

 

 
DOI no: 10.1021/cb700100n ACS Chem Biol 2:545-552 (2007)
PubMed id: 17696316  
 
 
A steric block in translation caused by the antibiotic spectinomycin.
M.A.Borovinskaya, S.Shoji, J.M.Holton, K.Fredrick, J.H.Cate.
 
  ABSTRACT  
 
The widely used antibiotic spectinomycin inhibits bacterial protein synthesis by blocking translocation of messenger RNA and transfer RNAs on the ribosome. Here, we show that in crystals of the Escherichia coli 70S ribosome spectinomycin binding traps a distinct swiveling state of the head domain of the small ribosomal subunit. Spectinomycin also alters the rate and completeness of reverse translocation in vitro. These structural and biochemical data indicate that in solution spectinomycin sterically blocks swiveling of the head domain of the small ribosomal subunit and thereby disrupts the translocation cycle.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21338423 C.C.Boutte, and S.Crosson (2011).
The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment.
  Mol Microbiol, 80, 695-714.  
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
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.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
21057527 J.B.Munro, M.R.Wasserman, R.B.Altman, L.Wang, and S.C.Blanchard (2010).
Correlated conformational events in EF-G and the ribosome regulate translocation.
  Nat Struct Mol Biol, 17, 1470-1477.  
19258531 B.A.Maguire (2009).
Inhibition of bacterial ribosome assembly: a suitable drug target?
  Microbiol Mol Biol Rev, 73, 22-35.  
19553343 B.Llano-Sotelo, R.P.Hickerson, L.Lancaster, H.F.Noller, and A.S.Mankin (2009).
Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.
  RNA, 15, 1597-1604.  
  19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
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.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
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
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.