Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

Science. 2001 Jun 8;292(5523):1863-76. doi: 10.1126/science.1059493. Epub 2001 Apr 19.


Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Conserved Sequence
  • Crystallography, X-Ray
  • DNA, Fungal / chemistry
  • DNA, Fungal / metabolism
  • Fourier Analysis
  • Hydrogen Bonding
  • Magnesium / metabolism
  • Metals / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Promoter Regions, Genetic
  • Protein Conformation
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Protein Subunits
  • RNA Polymerase II / chemistry*
  • RNA Polymerase II / metabolism*
  • RNA Processing, Post-Transcriptional
  • RNA, Fungal / biosynthesis
  • RNA, Fungal / chemistry
  • RNA, Fungal / metabolism
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic*


  • DNA, Fungal
  • Metals
  • Protein Subunits
  • RNA, Fungal
  • RNA, Messenger
  • Transcription Factors
  • RNA Polymerase II
  • Magnesium

Associated data

  • PDB/1I3Q
  • PDB/1I50