Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex

Structure. 2003 Jan;11(1):43-53. doi: 10.1016/s0969-2126(02)00934-6.


Aminoglycoside antibiotics that bind to 16S ribosomal RNA in the aminoacyl-tRNA site (A site) cause misreading of the genetic code and inhibit translocation. Structures of an A site RNA oligonucleotide free in solution and bound to the aminoglycosides paromomycin or gentamicin C1a have been determined by NMR. Recently, the X-ray crystal structure of the entire 30S subunit has been determined, free and bound to paromomycin. Distinct differences were observed in the crystal structure, particularly at A1493. Here, the NMR structure of the oligonucleotide-paromomycin complex was determined with higher precision and is compared with the X-ray crystal structure of the 30S subunit complex. The comparison shows the validity of both structures in identifying critical interactions that affect ribosome function.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • Gentamicins / chemistry
  • Gentamicins / metabolism
  • Macromolecular Substances
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation*
  • Oligoribonucleotides / chemistry
  • Oligoribonucleotides / metabolism
  • Paromomycin / chemistry*
  • Paromomycin / metabolism
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA, Ribosomal, 16S / chemistry*
  • RNA, Ribosomal, 16S / metabolism
  • RNA, Transfer, Amino Acyl / chemistry
  • RNA, Transfer, Amino Acyl / metabolism
  • Ribosomes / chemistry*
  • Ribosomes / metabolism


  • Anti-Bacterial Agents
  • Gentamicins
  • Macromolecular Substances
  • Oligoribonucleotides
  • Protein Subunits
  • RNA, Ribosomal, 16S
  • RNA, Transfer, Amino Acyl
  • Paromomycin