Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis

RNA. 2002 Apr;8(4):426-39. doi: 10.1017/s1355838202021088.


We describe characterization of spliceosomes affinity purified under native conditions. These spliceosomes consist largely of C complex containing splicing intermediates. After C complex assembly on an MS2 affinity-tagged pre-mRNA substrate containing a 3' splice site mutation, followed by RNase H digestion of earlier complexes, spliceosomes were purified by size exclusion and affinity selection. This protocol yielded 40S C complexes in sufficient quantities to visualize in negative stain by electron microscopy. Complexes purified in this way contain U2, U5, and U6 snRNAs, but very little U1 or U4 snRNA. Analysis by tandem mass spectrometry confirmed the presence of core snRNP proteins (SM and LSM), U2 and U5 snRNP-specific proteins, and the second step factors Prp16, Prp17, Slu7, and Prp22. In contrast, proteins specific to earlier splicing complexes, such as U2AF and U1 snRNP components, were not detected in C complex, but were present in similarly purified H complex. Images of these spliceosomes revealed single particles with dimensions of approximately 270 x 240 A that assort into well-defined classes. These images represent an important first step toward attaining a comprehensive three-dimensional understanding of pre-mRNA splicing.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Cell Cycle Proteins*
  • DEAD-box RNA Helicases
  • DNA-Binding Proteins*
  • Fungal Proteins / chemistry
  • Mass Spectrometry
  • Microscopy, Electron
  • RNA Helicases
  • RNA Precursors / chemistry
  • RNA Splicing
  • RNA Splicing Factors
  • RNA, Small Nuclear / chemistry
  • RNA-Binding Proteins / chemistry
  • Ribonuclease H / chemistry
  • Ribonuclease H / metabolism
  • Ribonucleoproteins, Small Nuclear*
  • Saccharomyces cerevisiae Proteins*
  • Spliceosomes / chemistry*


  • CDC40 protein, S cerevisiae
  • Cell Cycle Proteins
  • DNA-Binding Proteins
  • Fungal Proteins
  • RNA Precursors
  • RNA Splicing Factors
  • RNA, Small Nuclear
  • RNA-Binding Proteins
  • Ribonucleoproteins, Small Nuclear
  • SLU7 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • U2 small nuclear RNA
  • U6 small nuclear RNA
  • Ribonuclease H
  • Adenosine Triphosphatases
  • PRP16 protein, S cerevisiae
  • PRP2 protein, S cerevisiae
  • DEAD-box RNA Helicases
  • RNA Helicases