Structural basis of initial RNA polymerase II transcription

EMBO J. 2011 Nov 4;30(23):4755-63. doi: 10.1038/emboj.2011.396.


During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • DNA / metabolism
  • Lysine / metabolism
  • Models, Molecular
  • Nucleotides / metabolism
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / metabolism
  • RNA Polymerase II* / chemistry
  • RNA Polymerase II* / metabolism
  • RNA Polymerase II* / ultrastructure
  • Saccharomyces cerevisiae / enzymology
  • Transcription, Genetic / physiology*
  • Transcriptional Elongation Factors / metabolism


  • Nucleotides
  • Transcriptional Elongation Factors
  • RNA
  • DNA
  • RNA Polymerase II
  • Lysine