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PDBsum entry 2qoz

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2qoz
Jmol
Contents
Protein chains
141 a.a. *
271 a.a. *
209 a.a. *
121 a.a. *
114 a.a. *
201 a.a. *
58 a.a. *
56 a.a. *
38 a.a. *
50 a.a. *
64 a.a. *
94 a.a. *
46 a.a. *
143 a.a. *
136 a.a. *
63 a.a. *
149 a.a. *
142 a.a. *
120 a.a. *
116 a.a. *
117 a.a. *
110 a.a. *
102 a.a. *
178 a.a. *
176 a.a. *
103 a.a. *
93 a.a. *
77 a.a. *
79 a.a. *
DNA/RNA
Ligands
NMY
Metals
_ZN
_MG ×110
Waters ×506
* Residue conservation analysis
PDB id:
2qoz
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin and neomycin. This file contains the 50s subunit of the first 70s ribosome, with neomycin bound. The entire crystal structure contains two 70s ribosomes.
Structure: 5s rrna. Chain: a. 23s rrna. Chain: b. 50s ribosomal protein l11. Chain: i. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.
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 ?
P0A7K0  (RL11_SALTY) -  50S ribosomal protein L11
Seq:
Struc:
142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2
Seq:
Struc:
273 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3
Seq:
Struc:
209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14
Seq:
Struc:
123 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19
Seq:
Struc:
115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P60724  (RL4_ECOL6) -  50S ribosomal protein L4
Seq:
Struc:
201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30
Seq:
Struc:
59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N5  (RL32_ECO57) -  50S ribosomal protein L32
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36
Seq:
Struc:
38 a.a.
38 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P1  (RL33_ECO57) -  50S ribosomal protein L33
Seq:
Struc:
55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P9  (RL34_SALTI) -  50S ribosomal protein L34
Seq:
Struc:
46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15
Seq:
Struc:
144 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16
Seq:
Struc:
136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc:
63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13
Seq:
Struc:
142 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17
Seq:
Struc:
127 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18
Seq:
Struc:
117 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L7  (RL20_SALTI) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P61179  (RL22_SALTY) -  50S ribosomal protein L22
Seq:
Struc:
110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24
Seq:
Struc:
104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
A7ZSJ7  (RL5_ECO24) -  50S ribosomal protein L5
Seq:
Struc:
179 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6
Seq:
Struc:
177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21
Seq:
Struc:
103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23
Seq:
Struc:
100 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28
Seq:
Struc:
78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
79 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     response to antibiotic   6 terms 
  Biochemical function     structural constituent of ribosome     10 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.