Biochemistry I   Spring & Fall Terms

Yeast RNA Polymerase II Elongation Complex

  Rotate:
  Y 90°   Y -90°
  X 90°   X -90°

  Distances:
  Height (Å)
  Width (Å)

  Separate Structures
  DNA-RNA alone

  Background Color:
  White
  Blue
  Black

  Reset orientation.
  Remove labels.

Saccharomyces cerevisiae RNA Polymerase II Elongation Complex.
The yeast RNA Pol II is composed of ten subunits in this model. The protein chains are displayed as Backbone with colors matching Fig. 10.16 in Campbell. The molecular weight of the enzyme is 490 kDa.
The DNA template (cyan) and the nascent RNA transcript (green) are shown Spacefill.
(cf. Fig. 10.16 in Campbell where a non-elongating enzyme-DNA complex is shown.)

The three largest subunits (and their E. coli homologs) are colored as follows:
RPB1 (b'): Gray, Chain A
RPB2 (b): Gold, Chain B
RPB3 (a): Red, Chain C
The RNA (top strand) and DNA (bottom strand) sequences in the model are:
5' GACCAGGCA3'
3'TCTGGTCCGTAAA5'
The "DNA-RNA alone" button zooms in to view the DNA strand (labeled at the 5* end) and the RNA strand (labeled at the 3* end) in an A-form double helix with H-bonds colored yellow. In the next reaction step UTP would bind and pair with the dA nucleotide on the template strand. A phosphodiester bond would be formed; the RNA chain would be elongated to 10 nucleotides; and PPi would dissociate.

Note: The coordinates used in this display have only the alpha carbons of the proteins (CA). Thus, Backbone and Spacefill are the only Chime display options available. The published coordinates (1i6h.pdb) contain all of the side chain residues. See Gnatt, et al. below for a detailed description.

This structure is described in Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A., Kornberg, R. D. (2001) "Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution" Science 292:1876.     PubMed Abstract.

Back to the Protein Structure List.

smBack Return to Home Page Fall 2004 -or- Home Page Spring 2004.

8.21.04