Complex Between Neamine and the 16S-RRNA A-Site

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2005-10-27 Released: 2005-12-13 
  • Deposition Author(s): Westhof, E.

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

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Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.

Francois, B.Russell, R.J.Murray, J.B.Aboul-ela, F.Masquida, B.Vicens, Q.Westhof, E.

(2005) Nucleic Acids Res 33: 5677-5690

  • DOI: https://doi.org/10.1093/nar/gki862
  • Primary Citation of Related Structures:  
    2ESI, 2ESJ, 2ET3, 2ET4, 2ET5, 2ET8

  • PubMed Abstract: 

    The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson-Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.

  • Organizational Affiliation

    Institut de biologie moléculaire et cellulaire du CNRS, UPR9002 Architecture et Réactivité de l'ARN, Université Louis Pasteur, F-67084 Strasbourg, France.


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Entity ID: 1
MoleculeChains LengthOrganismImage
A, B
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on XXX

Download Ideal Coordinates CCD File 
C [auth B](1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
C12 H26 N4 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.055α = 90
b = 47.31β = 90
c = 85.343γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2005-12-13 
  • Deposition Author(s): Westhof, E.

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary