Eukaryotic RNA Polymerase II

  • David A. Bushnell
  • Roger D. Kornberg
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 30)


Structures of yeast RNA polymerase II, alone and in the act of transcription with associated DNA and RNA, have been determined to near-atomic resolution. The structures illuminate the basis for the fidelity of transcription, for translocation on the DNA template, and for release of the product RNA. Structures of an RNA polymerase II-general transcription factor complex have led to a model for a closed transcription initiation complex and have suggested a possible basis for promoter escape.


Yeast RNA polymerase II structure X-ray crystallography Trigger loop Nucleotide addition TFIIB 


  1. Armache KJ, Kettenberger H, Cramer P (2003) Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci USA 100(12):6964–6968PubMedCrossRefGoogle Scholar
  2. Buratowski S, Zhou H (1993) Functional domains of transcription factor TFIIB. Proc Natl Acad Sci USA 90(12):5633–5637PubMedCrossRefGoogle Scholar
  3. Bushnell DA, Kornberg RD (2003) Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci USA 100(12):6969–6973PubMedCrossRefGoogle Scholar
  4. Bushnell DA, Cramer P, Kornberg RD (2002) Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci USA 99(3):1218–1222PubMedCrossRefGoogle Scholar
  5. Bushnell DA, Westover KD, Davis RE, Kornberg RD (2004) Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 303(5660):983–988PubMedCrossRefGoogle Scholar
  6. Castro C, Smidansky ED, Arnold JJ, Maksimchuk KR, Moustafa I, Uchida A, Götte M, Konigsberg W, Cameron CE (2009) Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat Struct Mol Biol 16(2):212–218PubMedCrossRefGoogle Scholar
  7. Choder M, Young RA (1993) A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol Cell Biol 13(11):6984–6991PubMedGoogle Scholar
  8. Cramer P, Bushnell DA, Fu J, Gnatt AL, Maier-Davis B, Thompson NE, Burgess RR, Edwards AM, David PR, Kornberg RD (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640–649PubMedCrossRefGoogle Scholar
  9. Cramer P, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292(5523):1863–1876PubMedCrossRefGoogle Scholar
  10. Darst SA, Ribi HO, Pierce DW, Kornberg RD (1988) Two-dimensional crystals of Escherichia coli RNA polymerase holoenzyme on positively charged lipid layers. J Mol Biol 203(1):269–273PubMedCrossRefGoogle Scholar
  11. Darst SA, Kubalek EW, Kornberg RD (1989) Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature 340(6236):730–732PubMedCrossRefGoogle Scholar
  12. Darst SA, Kubalek EW, Edwards AM, Kornberg RD (1991a) Two-dimensional and epitaxial crystallization of a mutant form of yeast RNA polymerase II. J Mol Biol 221(1):347–357PubMedCrossRefGoogle Scholar
  13. Darst SA, Edwards AM, Kubalek EW, Kornberg RD (1991b) Three-dimensional structure of yeast RNA polymerase II at 16 A resolution. Cell 66(1):121–128PubMedCrossRefGoogle Scholar
  14. Epshtein V, Mustaev A, Markovtsov V, Bereshchenko O, Nikiforov V, Goldfarb A (2002) Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol Cell 10(3):623–634PubMedCrossRefGoogle Scholar
  15. Fu J, Gnatt AL, Bushnell DA, Jensen GJ, Thompson NE, Burgess RR, David PR, Kornberg RD (1999) Yeast RNA polymerase II at 5 A resolution. Cell 98(6):799–810PubMedCrossRefGoogle Scholar
  16. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292(5523):1876–1882PubMedCrossRefGoogle Scholar
  17. Ha I, Roberts S, Maldonado E, Sun X, Kim LU, Green M, Reinberg D (1993) Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev 7(6):1021–1032PubMedCrossRefGoogle Scholar
  18. Kaplan CD, Larsson K-M, Kornberg RD (2008) The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by α-amanitin. Mol Cell 30(5):547–556PubMedCrossRefGoogle Scholar
  19. Kaplan CD, Jin H, Zhang IL, Belyanin A (2012) Dissection of pol II trigger loop function and pol II activity-dependent control of start site selection in vivo. PLoS Genet 8(4):e1002627PubMedCrossRefGoogle Scholar
  20. Kireeva ML, Komissarova N, Waugh DS, Kashlev M (2000) The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem 275(9):6530–6536PubMedCrossRefGoogle Scholar
  21. Kolodziej PA, Woychik N, Liao SM, Young RA (1990) RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol 10(5):1915–1920PubMedGoogle Scholar
  22. Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, Cramer P (2009) RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462(7271):323–330PubMedCrossRefGoogle Scholar
  23. Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD (2010) Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327(5962):206–209PubMedCrossRefGoogle Scholar
  24. Poglitsch CL, Meredith GD, Gnatt AL, Jensen GJ, Chang WH, Fu J, Kornberg RD (1999) Electron crystal structure of an RNA polymerase II transcription elongation complex. Cell 98(6):791–798PubMedCrossRefGoogle Scholar
  25. Sosunov V, Sosunova E, Mustaev A, Bass I, Nikiforov V, Goldfarb A (2003) Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J 22(9):2234–2244PubMedCrossRefGoogle Scholar
  26. Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N et al (2005) Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 19(5):655–666PubMedCrossRefGoogle Scholar
  27. Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD Jr et al (2005) Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122(4):541–552PubMedCrossRefGoogle Scholar
  28. Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R (2007) Structural basis for substrate loading in bacterial RNA polymerase. Nature 448(7150):163–168PubMedCrossRefGoogle Scholar
  29. Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127(5):941–954PubMedCrossRefGoogle Scholar
  30. Westover KD, Bushnell DA, Kornberg RD (2004a) Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303(5660):1014–1016PubMedCrossRefGoogle Scholar
  31. Westover KD, Bushnell DA, Kornberg RD (2004b) Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119(4):481–489PubMedCrossRefGoogle Scholar
  32. Wieland T, Faulstich H (1991) Fifty years of amanitin. Experientia 47(11–12):1186–1193PubMedCrossRefGoogle Scholar
  33. Yuzenkova Y, Bochkareva A, Tadigotla VR, Roghanian M, Zorov S, Severinov K, Zenkin N (2010) Stepwise mechanism for transcription fidelity. BMC Biol 8(1):54PubMedCrossRefGoogle Scholar
  34. Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 98(6):811–824PubMedCrossRefGoogle Scholar
  35. Zhang J, Palangat M, Landick R (2009) Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol 17(1):99–104PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Stanford University School of MedicineStanfordUSA

Personalised recommendations