User:Jordan Scott/Sandbox RNA polII

From Proteopedia

Jump to: navigation, search

Yeast RNA Polymerase II complex with RNA (PDB code 1i6h)


  1. 1.0 1.1 1.2 Young RA. RNA polymerase II. Annu Rev Biochem. 1991;60:689-715. doi: 10.1146/ PMID:1883205 doi:
  2. 2.0 2.1 Myer VE, Young RA. RNA polymerase II holoenzymes and subcomplexes. J Biol Chem. 1998 Oct 23;273(43):27757-60. doi: 10.1074/jbc.273.43.27757. PMID:9774381 doi:
  3. 3.0 3.1 3.2 Sobennikova MV, Shematorova EK, Shpakovskii GV. [C-terminal domain (CTD) of the subunit Rpb1 of nuclear RNA polymerase II and its role in the transcription cycle]. Mol Biol (Mosk). 2007 May-Jun;41(3):433-49. PMID:17685222
  4. 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 RNA polymerase II transcription initiation: A structural view D. B. Nikolov, S. K. Burley Proceedings of the National Academy of Sciences Jan 1997, 94 (1) 15-22; DOI: 10.1073/pnas.94.1.15
  5. Hurwitz J. The discovery of RNA polymerase. J Biol Chem. 2005 Dec 30;280(52):42477-85. doi: 10.1074/jbc.X500006200. Epub 2005, Oct 17. PMID:16230341 doi:
  6. doi:

(A)Young, Richard A. (2003-11-28). "RNA Polymerase II". Annual Review of Biochemistry. 60 (1): 689–715. doi:10.1146/ PMID 1883205. (G) C-terminal domain of subunit Rpb1 of nuclear RNA polymerase II and its role in the transcription cycle

(B) RNA Polymerase II Holoenzymes and Subcomplexes

(C) RNA polymerase II transcription initiation: A structural view

(D)The Discovery and Isolation of RNA Polymerase by Jerard HurwiMultiple forms of DNA-dependent RNA polymerase in eukaryotic organismstz



(F)The general transcription factors of RNA polymerase II

(H)Interactions between the Human RNA Polymerase II Subunits*

Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988

Brueckner, F. and Cramer, P. Structural Basis of Transcription Inhibition by -amanitin and Implications for RNA Polymerase II Translocation. Nature Structure and Molecular Biology. 2008, 15, 811-818.

Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876

Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.

Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h

Hahn, S. Structure and Mechanism of the RNA Polymerase II Transcription Machinery. Nature Structure and Molecular Biology. 2004, 11, 394-403.

He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.

Nudler, E. RNA Polymerase Active Center: The Molecular Engine of Transcription. Annu. Rev. Biochem. 2009, 78, 335-361.

Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683

Shah, N. et. al. Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals. Molecular Cell. 2018, 69, 48-61.

Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.

Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr

Xin, L.; Bushnell, D. A.; and Kornburg, R. D. RNA Polymerase II Transcription: Structure and Mechanism. Biochemica et Biophysica Acta. 2013, 1829, 2-8.

Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.

Alpha-aminitin chemical structure image courtesy of


From structural components:

Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]

Bridge: Depicted: [PDB: 1I6H: 810-845.a]

Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]

Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]

Rudder: Depicted: [PDB: 5VVR: 306-321.a]

Content Donators

This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.

Proteopedia Page Contributors and Editors (what is this?)

Jordan Scott

Personal tools