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Originally published in Science Express on 19 April 2001
Science 8 June 2001:
Vol. 292. no. 5523, pp. 1876 - 1882
DOI: 10.1126/science.1059495
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Research Articles

Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution

Averell L. Gnatt,* Patrick Cramer,dagger Jianhua Fu,ddagger 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.

dagger    Present address: Institute of Biochemistry, Gene Center, University of Munich, 81377 Munich, Germany.

ddagger    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

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Complete, 12-subunit RNA polymerase II at 4.1-A resolution: Implications for the initiation of transcription.
D. A. Bushnell and R. D. Kornberg (2003)
PNAS 100, 6969-6973
   Abstract »    Full Text »    PDF »
RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins.
T. J. Santangelo, R. A. Mooney, R. Landick, and J. W. Roberts (2003)
Genes & Dev. 17, 1281-1292
   Abstract »    Full Text »    PDF »
The initiation-elongation transition: Lateral mobility of RNA in RNA polymerase II complexes is greatly reduced at +8/+9 and absent by +23.
M. Pal and D. S. Luse (2003)
PNAS 100, 5700-5705
   Abstract »    Full Text »    PDF »
Heterogeneous nuclear ribonucleoprotein (hnRNP) binding to hormone response elements: A cause of vitamin D resistance.
H. Chen, M. Hewison, B. Hu, and J. S. Adams (2003)
PNAS 100, 6109-6114
   Abstract »    Full Text »    PDF »
NTP-driven Translocation by Human RNA Polymerase II.
Y. A. Nedialkov, X. Q. Gong, S. L. Hovde, Y. Yamaguchi, H. Handa, J. H. Geiger, H. Yan, and Z. F. Burton (2003)
J. Biol. Chem. 278, 18303-18312
   Abstract »    Full Text »    PDF »
Cooperation Between RNA Polymerase Molecules in Transcription Elongation.
V. Epshtein and E. Nudler (2003)
Science 300, 801-805
   Abstract »    Full Text »    PDF »


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