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PDBsum entry 3knm
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protein dna_rna metals Protein-protein interface(s) links
Ribosome/antibiotic PDB id
3knm

 

 

 

 

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Contents
Protein chains
191 a.a. *
272 a.a. *
205 a.a. *
206 a.a. *
181 a.a. *
161 a.a. *
146 a.a. *
139 a.a. *
122 a.a. *
146 a.a. *
139 a.a. *
117 a.a. *
99 a.a. *
138 a.a. *
117 a.a. *
101 a.a. *
113 a.a. *
93 a.a. *
88 a.a. *
177 a.a. *
84 a.a. *
94 a.a. *
71 a.a. *
60 a.a. *
49 a.a. *
59 a.a. *
48 a.a. *
49 a.a. *
64 a.a. *
36 a.a. *
DNA/RNA
Metals
_MG ×359
_ZN ×3
* Residue conservation analysis
Obsolete entry
PDB id:
3knm
Name: Ribosome/antibiotic
Title: The structures of capreomycin bound to the 70s ribosome. This file contains the 50s subunit for molecule i.
Structure: 23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l1. Chain: c. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
3.45Å     R-factor:   0.218     R-free:   0.268
Authors: R.E.Stanley,G.Blaha
Key ref: R.E.Stanley et al. (2010). The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Biol, 17, 289-293. PubMed id: 20154709
Date:
12-Nov-09     Release date:   16-Feb-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SLP7  (RL1_THET8) -  50S ribosomal protein L1 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		229 a.a.
191 a.a.
Protein chain
Pfam   ArchSchema ?
P60405  (RL2_THET8) -  50S ribosomal protein L2 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		276 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN8  (RL3_THET8) -  50S ribosomal protein L3 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN9  (RL4_THET8) -  50S ribosomal protein L4 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		210 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ0  (RL5_THET8) -  50S ribosomal protein L5 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		182 a.a.
181 a.a.
Protein chain
Q5SHQ3  (RL6_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SLQ1  (RL9_THET8) -  50S ribosomal protein L9 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		148 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60488  (RL13_THET8) -  50S ribosomal protein L13 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		140 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP8  (RL14_THET8) -  50S ribosomal protein L14 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ7  (RL15_THET8) -  50S ribosomal protein L15 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60489  (RL16_THET8) -  50S ribosomal protein L16 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		141 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Z9H5  (RL17_THET8) -  50S ribosomal protein L17 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ4  (RL18_THET8) -  50S ribosomal protein L18 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		112 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P60490  (RL19_THET8) -  50S ribosomal protein L19 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		146 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P60491  (RL20_THET8) -  50S ribosomal protein L20 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P60492  (RL21_THET8) -  50S ribosomal protein L21 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		113 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP0  (RL23_THET8) -  50S ribosomal protein L23 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		96 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP9  (RL24_THET8) -  50S ribosomal protein L24 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		110 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHZ1  (RL25_THET8) -  50S ribosomal protein L25 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		206 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P60493  (RL27_THET8) -  50S ribosomal protein L27 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P60494  (RL28_THET8) -  50S ribosomal protein L28 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		98 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP6  (RL29_THET8) -  50S ribosomal protein L29 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		72 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		60 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJE1  (RL31_THET8) -  50S ribosomal protein L31 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		71 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
P80339  (RL32_THET8) -  50S ribosomal protein L32 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
P35871  (RL33_THET8) -  50S ribosomal protein L33 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		54 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		49 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKU1  (RL35_THET8) -  50S ribosomal protein L35 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHR2  (RL36_THET8) -  50S ribosomal protein L36 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Seq:
Struc: 		37 a.a.
36 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-G-A-U-G-G-U-A-A-G-G-G-C-C-C-A-C-G-G-U-G-G-A-U-G-C-C-U-C-G-G-C-A-C-C-C-G-A-G- ... 2789 bases
  U-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-G-G-C-G-U-G-G-A-A-C-C-A-C-C-C-G-U-U-C-C-C-A- 119 bases

 

 
Nat Struct Biol 17:289-293 (2010)
PubMed id: 20154709  
 
 
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, T.A.Steitz.
 
  ABSTRACT  
 
Viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. Here we present two crystal structures of the 70S ribosome in complex with three tRNAs and bound to either viomycin or capreomycin at 3.3- and 3.5-A resolution, respectively. Both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ribosomal subunit. The structures of these complexes suggest that the tuberactinomycins inhibit translocation by stabilizing the tRNA in the A site in the pretranslocation state. In addition, these structures show that the tuberactinomycins bind adjacent to the binding sites for the paromomycin and hygromycin B antibiotics, which may enable the development of new derivatives of tuberactinomycins that are effective against drug-resistant strains.
 

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
21427106 A.Engström, N.Perskvist, J.Werngren, S.E.Hoffner, and P.Juréen (2011).
Comparison of clinical isolates and in vitro selected mutants reveals that tlyA is not a sensitive genetic marker for capreomycin resistance in Mycobacterium tuberculosis.
  J Antimicrob Chemother, 66, 1247-1254.  
21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
  Biophys J, 100, 2201-2208.  
22020300 P.K.Khade, and S.Joseph (2011).
Messenger RNA interactions in the decoding center control the rate of translocation.
  Nat Struct Mol Biol, 18, 1300-1302.  
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.  
20876130 D.Bulkley, C.A.Innis, G.Blaha, and T.A.Steitz (2010).
Revisiting the structures of several antibiotics bound to the bacterial ribosome.
  Proc Natl Acad Sci U S A, 107, 17158-17163.
PDB codes: 3oge 3ogy 3oh5 3oh7 3ohc 3ohd 3ohj 3ohk 3ohy 3ohz 3oi0 3oi1 3oi2 3oi3 3oi4 3oi5
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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