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Nucleic Acids Res. 2016 Oct 14;44(18):8976-8989. Epub 2016 Jun 24.

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

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1
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
2
Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA RIKEN Center for Life Science Technology, Yokohama, Kanagawa 230-0045, Japan.
3
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
4
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Genetics, Yale University, New Haven, CT 06520, USA Department of Therapeutic Radiology, Yale University, New Haven, CT 06520, USA susan.baserga@yale.edu.

Abstract

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.

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