Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution
Averell L. Gnatt,*
Patrick Cramer,
Jianhua Fu,
David A. Bushnell,
Roger D. Kornberg§
The crystal structure of RNA polymerase II in the act of
transcription was determined at 3.3 Å resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active
site. Nine base pairs of DNA-RNA hybrid extend from the active center
at nearly right angles to the entering DNA, with the 3' end of the RNA
in the nucleotide addition site. The 3' end is positioned above a pore,
through which nucleotides may enter and through which RNA may be
extruded during back-tracking. The 5'-most residue of the RNA is close
to the point of entry to an exit groove. Changes in protein structure
between the transcribing complex and free enzyme include closure of a
clamp over the DNA and RNA and ordering of a series of "switches"
at the base of the clamp to create a binding site complementary to the
DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA
translocation during transcription elongation.
Department of Structural Biology, Stanford University School of
Medicine, Stanford, CA 94305-5126, USA.
*
Present address: Department of Pharmacology and Experimental
Therapy, University of Maryland, 655 West Baltimore Street, HH403, Baltimore, MD 21201, USA.
Present address: Institute of Biochemistry, Gene
Center, University of Munich, 81377 Munich, Germany.
Present address: Department of Molecular Biology and
Genetics, Cornell University, 223 Biotechnology Building, Ithaca, NY 14853, USA.
§
To whom correspondence should be addressed. E-mail:
kornberg{at}stanford.edu
