Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs

Nucleic Acids Res. 2016 Oct 14;44(18):8976-8989. doi: 10.1093/nar/gkw576. Epub 2016 Jun 24.


Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2'-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture.

MeSH terms

  • Archaea / genetics
  • Cryoelectron Microscopy
  • Magnetic Resonance Spectroscopy
  • Methylation
  • Models, Molecular
  • Mutation
  • Nucleic Acid Conformation*
  • Protein Binding
  • Protein Conformation
  • RNA Stability
  • RNA Transport
  • RNA, Archaeal / chemistry
  • RNA, Archaeal / genetics
  • RNA, Ribosomal / chemistry*
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism*
  • Ribonucleoproteins, Small Nucleolar / metabolism*


  • RNA, Archaeal
  • RNA, Ribosomal
  • Ribonucleoproteins, Small Nucleolar