Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors


During transcription, RNA polymerase (Pol) II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing by the carboxy-terminal domain (CTD) of Pol II, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7 (refs 1, 2). After phosphorylation, the CTD binds tightly to a conserved CTD-interacting domain (CID) present in the proteins Pcf11 and Nrd1, which are essential and evolutionarily conserved factors for polyadenylation-dependent and -independent 3′-RNA processing, respectively. Here we describe the structure of a Ser 2-phosphorylated CTD peptide bound to the CID domain of Pcf11. The CTD motif Ser 2-Pro 3-Thr 4-Ser 5 forms a β-turn that binds to a conserved groove in the CID domain. The Ser 2 phosphate group does not make direct contact with the CID domain, but may be recognized indirectly because it stabilizes the β-turn with an additional hydrogen bond. Iteration of the peptide structure results in a compact β-spiral model of the CTD. The model suggests that, during the mRNA transcription-processing cycle, compact spiral regions in the CTD are unravelled and regenerated in a phosphorylation-dependent manner.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Structure of the CID–CTD complex.
Figure 2: CTD–CID interactions.
Figure 3: CTD β-spiral model.


  1. 1

    Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000)

    CAS  Google Scholar 

  2. 2

    Proudfoot, N. J., Furger, A. & Dye, M. J. Integrating mRNA processing with transcription. Cell 108, 501–512 (2002)

    CAS  Article  Google Scholar 

  3. 3

    Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8Ångstrom resolution. Science 292, 1863–1876 (2001)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Komarnitsky, P., Cho, E. J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452–2460 (2000)

    CAS  Article  Google Scholar 

  5. 5

    Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13, 67–76 (2004)

    CAS  Article  Google Scholar 

  6. 6

    Ni, Z., Schwartz, B. E., Werner, J., Suarez, J. R. & Lis, J. T. Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol. Cell 13, 55–65 (2004)

    CAS  Article  Google Scholar 

  7. 7

    Buratowski, S. The CTD code. Nature Struct. Biol. 10, 679–680 (2003)

    CAS  Article  Google Scholar 

  8. 8

    Yuryev, A. et al. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl Acad. Sci. USA 93, 6975–6980 (1996)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Patturajan, M., Wei, X., Berezney, R. & Corden, J. L. A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Mol. Cell. Biol. 18, 2406–2415 (1998)

    CAS  Article  Google Scholar 

  10. 10

    Steinmetz, E. J., Conrad, N. K., Brow, D. A. & Corden, J. L. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413, 327–331 (2001)

    ADS  CAS  Article  Google Scholar 

  11. 11

    Barilla, D., Lee, B. A. & Proudfoot, N. J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 98, 445–450 (2001)

    ADS  CAS  PubMed  Google Scholar 

  12. 12

    Misra, S., Puertollano, R., Kato, Y., Bonifacino, J. S. & Hurley, J. H. Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains. Nature 415, 933–937 (2002)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Conti, E., Uy, M., Leighton, L., Blobel, G. & Kuriyan, J. Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin α. Cell 94, 193–204 (1998)

    CAS  Article  Google Scholar 

  14. 14

    Sadowski, M., Dichtl, B., Hubner, W. & Keller, W. Independent functions of yeast Pcf11p in pre-mRNA 3′ end processing and in transcription termination. EMBO J. 22, 2167–2177 (2003)

    CAS  Article  Google Scholar 

  15. 15

    West, M. L. & Corden, J. L. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140, 1223–1233 (1995)

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Suzuki, M. SPXX, a frequent sequence motif in gene regulatory proteins. J. Mol. Biol. 207, 61–84 (1989)

    CAS  Article  Google Scholar 

  17. 17

    Licatalosi, D. D. et al. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell 9, 1101–1111 (2002)

    CAS  Article  Google Scholar 

  18. 18

    Verdecia, M. A., Bowman, M. E., Lu, K. P., Hunter, T. & Noel, J. P. Structural basis for phosphoserine–proline recognition by group IV WW domains. Nature Struct. Biol. 7, 639–643 (2000)

    CAS  Article  Google Scholar 

  19. 19

    Fabrega, C., Shen, V., Shuman, S. & Lima, C. D. Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Mol. Cell 11, 1549–1561 (2003)

    CAS  Article  Google Scholar 

  20. 20

    Kumaki, Y., Matsushima, N., Yoshida, H., Nitta, K. & Hikichi, K. Structure of the YSPTSPS repeat containing two SPXX motifs in the CTD of RNA polymerase II: NMR studies of cyclic model peptides reveal that the SPTS turn is more stable than SPSY in water. Biochim. Biophys. Acta. 1548, 81–93 (2001)

    CAS  Article  Google Scholar 

  21. 21

    Cagas, P. M. & Corden, J. L. Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II. Proteins 21, 149–160 (1995)

    CAS  Article  Google Scholar 

  22. 22

    Meredith, G. D. et al. The C-terminal domain revealed in the structure of RNA polymerase II. J. Mol. Biol. 258, 413–419 (1996)

    CAS  Article  Google Scholar 

  23. 23

    Zhang, J. & Corden, J. L. Phosphorylation causes a conformational change in the carboxyl-terminal domain of the mouse RNA polymerase II largest subunit. J. Biol. Chem. 266, 2297–2302 (1991)

    CAS  PubMed  Google Scholar 

  24. 24

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  25. 25

    Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993)

    CAS  Article  Google Scholar 

  26. 26

    Smith, G. D., Nagar, B., Rini, J. M., Hauptman, H. A. & Blessing, R. H. The use of SnB to determine an anomalous scattering substructure. Acta. Crystallogr. D 54, 799–804 (1998)

    CAS  Article  Google Scholar 

  27. 27

    Terwilliger, T. C. Automated structure solution, density modification and model building. Acta. Crystallogr. 58, 1937–1940 (2002)

    Article  Google Scholar 

  28. 28

    Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta. Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  29. 29

    Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta. Crystallogr. D 54, 905–921 (1998)

    Article  Google Scholar 

  30. 30

    Armache, K. J., Kettenberger, H. & Cramer, P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl Acad. Sci. USA 100, 6964–6968 (2003)

    ADS  CAS  Article  Google Scholar 

Download references


Part of this work was performed at the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. We thank C. Schulze-Briese and the staff of beamline X06SA for help; L. Jacquamet and J. McCarthy for help during data collection at the European Synchrotron Radiation Facility, Grenoble, France; G. Arnold for peptide synthesis; and K. Sträβer and members of the Cramer laboratory for careful reading of the manuscript. P.C. is supported by the Deutsche Forschungsgemeinschaft, the EMBO Young Investigator Programme and the Fonds der Chemischen Industrie. A.M. is supported by an EMBO long-term fellowship.

Author information



Corresponding author

Correspondence to Patrick Cramer.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Table 1

Structure determination and refinement statistics. (XLS 18 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Meinhart, A., Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing