Crystal structure of geneticin bound to the eubacterial 16S rRNA A site

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2002-09-30 Released: 2003-02-18 
  • Deposition Author(s): Vicens, Q., Westhof, E.

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

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Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide

Vicens, Q.Westhof, E.

(2003) J Mol Biol 326: 1175-1188

  • DOI: https://doi.org/10.1016/s0022-2836(02)01435-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.

  • Organizational Affiliation

    Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisation et simulations des Acides Nucléiques, UPR 9002, Université Louis Pasteur, 15 rue René Descartes, 67084 Cedex, Strasbourg, France.


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Entity ID: 1
MoleculeChains LengthOrganismImage
A, B
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 33.18β = 104.13
c = 51.74γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-18
    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
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description