Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3'-end processing factors

Nucleic Acids Res. 2010 May;38(9):3119-32. doi: 10.1093/nar/gkq002. Epub 2010 Jan 21.


Rna15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. CFIA is required for polyA site selection/cleavage targeting RNA sequences that surround polyadenylation sites in the 3'-UTR of RNA polymerase-II transcripts. RNA recognition by CFIA is mediated by an RNA recognition motif (RRM) contained in the Rna15 subunit of the complex. We show here that Rna15 has a strong and unexpected preference for GU containing RNAs and reveal the molecular basis for a base selectivity mechanism that accommodates G or U but discriminates against C and A bases. This mode of base selectivity is rather different to that observed in other RRM-RNA structures and is structurally conserved in CstF64, the mammalian counterpart of Rna15. Our observations provide evidence for a highly conserved mechanism of base recognition amongst the 3'-end processing complexes that interact with the U-rich or U/G-rich elements at 3'-end cleavage/polyadenylation sites.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Guanine
  • Models, Molecular
  • Mutation
  • Protein Binding
  • RNA / chemistry*
  • RNA / metabolism
  • RNA 3' End Processing
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Uracil
  • mRNA Cleavage and Polyadenylation Factors / chemistry*
  • mRNA Cleavage and Polyadenylation Factors / metabolism


  • Saccharomyces cerevisiae Proteins
  • mRNA Cleavage and Polyadenylation Factors
  • RNA15 protein, S cerevisiae
  • Uracil
  • Guanine
  • RNA

Associated data

  • PDB/2X1A
  • PDB/2X1B
  • PDB/2X1F