Three-dimensional model of yeast RNA polymerase I determined by electron microscopy of two-dimensional crystals

EMBO J. 1993 Jul;12(7):2601-7. doi: 10.1002/j.1460-2075.1993.tb05920.x.

Abstract

Two-dimensional crystals of yeast RNA polymerase I dimers were obtained upon interaction with positively charged lipid layers. A three-dimensional surface model of the enzyme was determined by analyzing tilted crystalline areas and by taking advantage of the non-crystallographic internal symmetry of the dimer to correct for the missing viewing directions. The structure shows, at approximately 3 nm resolution, an irregularly shaped molecule 11 nm x 11 nm x 15 nm in size characterized by a 3 nm wide and 10 nm long groove which constitutes a putative DNA binding site. The overall structure is similar to the Escherichia coli holo enzyme and the yeast RNA polymerase II delta 4/7 structures. The most remarkable structural feature is a finger-shaped stalk which partially occludes the entrance of the groove and forms a 2.5 nm wide channel. We discuss the possible location of the catalytic centre and of the carboxy-terminal region of the beta-like subunit in the channel. The interference of different DNA fragments with RNA polymerase dimerization and crystallization indicates the orientation of the template in the putative DNA binding groove.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Crystallization
  • DNA / metabolism
  • Image Processing, Computer-Assisted
  • Microscopy, Electron
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • RNA Polymerase I / chemistry*
  • RNA Polymerase I / metabolism
  • RNA Polymerase I / ultrastructure
  • Saccharomyces cerevisiae / enzymology*
  • Sequence Alignment
  • Templates, Genetic

Substances

  • DNA
  • RNA Polymerase I