1LC4

Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2002-04-05 Released: 2003-04-08 
  • Deposition Author(s): Vicens, Q., Westhof, E.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of a Complex between the Aminoglycoside Tobramycin and an Oligonucleotide Containing the Ribosomal Decoding A Site

Vicens, Q.Westhof, E.

(2002) Chem Biol 9: 747-755

  • DOI: 10.1016/s1074-5521(02)00153-9
  • Primary Citation of Related Structures:  
    1LC4

  • PubMed Abstract: 
  • Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin ...

    Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin. The three aminosugar rings making up tobramycin interact with the deep-groove atoms directly or via water molecules and stabilize a fully bulged-out conformation of adenines A(1492) and A(1493). The comparison between this structure and the one previously solved in the presence of paromomycin confirms the importance of the functional groups on the common neamine part of these two antibiotics for binding to RNA. Furthermore, the analysis of the present structure provides a molecular explanation to some of the resistance mechanisms that have spread among bacteria and rendered aminoglycoside antibiotics inefficient.


    Related Citations: 
    • Crystal Structure of Paromomycin Docked into the Eubacterial Ribosomal Decoding A Site
      Vicens, Q., Westhof, E.
      (2001) Structure 9: 647

    Organizational Affiliation

    Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Modélisation et Simulations des Acides Nucléiques, UPR 9002, Université Louis Pasteur, 15 Rue René Descartes, 67084 Strasbourg Cedex, France.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'A, B23N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOY
Query on TOY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
TOBRAMYCIN
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.9α = 90
b = 32.8β = 107.9
c = 52γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-08
    Changes: Derived calculations