Evidence and sources

Measurements

Loading the measurements…

Big picture numbers

Structures

• 5C4X
  Yeast Pol II elongation complex with a complete bubble

  The complete transcription bubble in one entry: both DNA strands and the RNA, on all twelve subunits. X-ray diffraction, 4 Å.
• 1I50
  Free yeast Pol II, clamp open

  The clamp is open here, which lets straight DNA into the cleft. It is the start state for the clamp-closing morph. X-ray diffraction, 2.8 Å.
• 1I6H
  Yeast Pol II elongation complex, clamp closed

  The same ten subunits as the free enzyme, with nucleic acid bound and the clamp closed. It pairs with 1I50 for a morph. X-ray diffraction, 3.3 Å.
• 2E2H
  Pol II elongation complex with GTP in the active site

  Shows the substrate in the addition site, the state that closes the trigger loop over the nucleotide. X-ray diffraction, 3.95 Å.
• 2VUM
  Pol II elongation complex inhibited by alpha-amanitin

  The drug traps the enzyme with a shifted bridge helix and a wedged trigger loop, which shows how translocation is blocked. X-ray diffraction, 3.4 Å.
• 1K83
  Yeast Pol II with alpha-amanitin

  The first view of the amanitin site, next to the bridge helix. X-ray diffraction, 2.8 Å.
• 5FLM
  Mammalian Pol II elongation complex

  The mammalian enzyme in the act of transcribing, for a species comparison with yeast. Electron microscopy, 3.4 Å.
• 2O5I
  Bacterial RNA polymerase elongation complex

  The bacterial comparison: five subunit types instead of twelve, with the same two-metal active site. The DNA template is in the active site, ready to pair with substrate. X-ray diffraction, 2.5 Å.
• 2O5J
  Bacterial elongation complex with substrate analogue

  Same crystal form as 2O5I with substrate bound, so the trigger-loop folding step can be morphed. X-ray diffraction, 3 Å.
• 2PPB
  Bacterial elongation complex with streptolydigin

  Shows an inactive pre-insertion substrate position, the state an antibiotic can freeze. X-ray diffraction, 3 Å.
• 6RH3
  E. coli RNA polymerase elongation complex with CTP

  An E. coli elongation complex with clearly named template and non-template strands. Electron microscopy, 3.6 Å.
• 1MSW
  T7 RNA polymerase elongation complex

  The single-subunit phage enzyme used for orthogonal expression. It shows how small a working polymerase can be. X-ray diffraction, 2.1 Å.

References

1. 1Cramer et al., Science 2001
2. 2Gnatt et al., Science 2001
3. 3Bushnell and Kornberg, PNAS 2003
4. 4Bushnell et al., PNAS 2002
5. 5Brueckner and Cramer, Nature Structural and Molecular Biology 2008
6. 6Wang et al., Cell 2006
7. 7Vassylyev et al., Nature 2007, 448, 157-162
8. 8Vassylyev et al., Nature 2007, 448, 163-168
9. 9Sydow and Cramer, Current Opinion in Structural Biology 2009
10. 10Sydow et al., Molecular Cell 2009
11. 11Thomas et al., Cell 1998
12. 12Cheung and Cramer, Nature 2011
13. 13Barnes et al., Molecular Cell 2015
14. 14Bernecky et al., Nature 2016
15. 15Abdelkareem et al., Molecular Cell 2019
16. 16Yin and Steitz, Science 2002
17. 17Studier and Moffatt, Journal of Molecular Biology 1986
18. 18Singh and Padgett, Nature Structural and Molecular Biology 2009
19. 19Jonkers et al., eLife 2014
20. 20Gout et al., PNAS 2013