Publications

  1. Faylo J.L., van Eeuwen T., Kim H.J., Gorbea J., Garcia B.A., Murakami K. and Christianson D.W: Structural insight on assembly-line catalysis in terpene biosynthesis. Nature Communications 12: 3487, 2021.
  2. van Eeuwen T., Shim Y., Kim H.J., Zhao T., Basu S., Garcia B.A., Kaplan C.D., Min J.H., and Murakami K.: Cryo-EM structure of TFIIH/Rad4–Rad23–Rad33 in damaged DNA opening in nucleotide excision repair. Nature Communications 12: 3338, 2021.
  3. Yang C., Fujiwara R., Kim H.J., Gorbea J., Steimle S., Garcia B.A., and Murakami K.: Structural visualization of de novo initiation of RNA polymerase II transcriptionbioRxiv, 2021.
  4. van Eeuwen T., Li T., Kim H.J., Gorbea J., Parker M.I., Dunbrack R.L., Garcia B.A., Tsai K.L., and Murakami K.Structure of TFIIK for phosphorylation of CTD of RNA polymerase IIScience Advances: 7 (15): eabd4420, 2021
  5. ​​​​​​Steimle S., van Eeuwen T., Ozturk Y., Kim H.J., Braitbard M., Selamoglu N., Garcia B.A., Schneidman-Duhovny D., Murakami K., and Daldal F.:

    Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes. Nature Communications 12: 929, 2021.

  6. Li Y.C., Chao T.C., Kim H.J., Cholko T., Chen S.F., Li G., Snyder L., Nakanishi K., Chang C., Murakami K., Garcia B.A., Boyer T.G., and Tsai K.L., Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. Science Advances 7 (3): eabd4484, 2021.

  7. Zimmet A., van Eeuwen T., Boczkowska M., Rebowski G., Murakami K., and Dominguez R. : Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism.  Science Advances 6 (23): eaaz7651, 2020. 

  8. Fujiwara R., Damodaren N., Wilusz J.E., and Murakami K. : The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation. Proceedings of the National Academy of Sciences 116 (45): 22573-22582, 2019. highlighted

  9. Allu P.K., Dawicki-McKenna J.M., van Eeuwen T., Slavin M., Braitbard M., Xu C., Kalisman N., Murakami K., and Black B.E. : Structure of the human core centromeric nucleosome Complex. Current Biology 29 (16): 2625-2639. e5, 2019.

  10. Fujiwara R., Murakami K. : In vitro reconstitution of yeast RNA polymerase II transcription initiation with high efficiency. Methods 159-160: 82-89, 2019.

  11. Damodaren N., van Eeuwen T., Zamel J., Lin-Shiao E., Kalisman N., and Murakami K.: Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proceedings of the National Academy of Sciences 114 (50): 13230-13235, 2017.
  12. Tsai K.L., Yu X., Gopalan S., Chao T.C., Zhang Y., Florens L., Washburn M.P., Murakami K., Conaway R.C., Conaway J.W., and Asturias F.J. : Mediator structure and rearrangements required for holoenzyme formation. Nature 544 (7649): 196-201, 2017.
  13. Murakami K., Tsai K.L., Kalisman N., Bushnell D.A., Asturias F.J., and Kornberg R.D. : Structure of an RNA polymerase II preinitiation complex. Proceedings of the National Academy of Sciences 112 (44): 13543-13548, 2015.
  14. Fazal F.M., Meng C.A., Murakami K., Kornberg R.D., and Block S.M. : Real-time observation of the initiation of RNA polymerase II transcription. Nature 525 (7568): 274-277, 2015.
  15. Murakami K., Mattei P.J., Davis R.E., Jin H., Kaplan C.D., and Kornberg R.D. : Uncoupling promoter opening from start-site scanning. Molecular Cell 59 (1): 133–138, 2015.
  16. Schweikhard V., Meng C., Murakami K., Kaplan C.D., Kornberg R.D., and Block S.M. : Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proceedings of the National Academy of  Sciences 111 (18): 6642-6647, 2014.
  17. Pai D.A., Kaplan C.D., Kweon H.K., Murakami K., Andrews P.C., and Engelke D.R. : RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template. RNA 20 (5): 644-655, 2014.
  18. Murakami K., Elmlund, H., Kalisman N., Bushnell D.A., Adams C.M. Azubel M., Elmlund D., Levi-Kalisman Y., Liu X., Gibbons B.J., Levitt M., and Kornberg R.D. : Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342 (6159), 1238724, 2013.
  19. Murakami K., Calero G., Brown C.R., Liu X., Davis R.E., Boeger H., and Kornberg R.D. : Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. Journal of Biological Chemistry 288 (9): 6325-6332, 2013.
  20. Murakami K., Gibbons B.J., Davis R.E., Nagai S., Liu X., Robinson P.J., Wu T., Kaplan C.D., and Kornberg R.D. : Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation. Proceedings of the National Academy of Sciences 109 (13), 4816-4821, 2012.
  21. Gibbons B.J., Brignole E.J., Azubel M, Murakami K., Voss N.R., Bushnell D.A., Asturias F.J., and Kornberg R.D. : Subunit architecture of general transcription factor TFIIH. Proceedings of the National Academy of Sciences 109 (6): 1949-1954 2012.
  22. Murakami K., Yasunaga T., Noguchi T.Q., Gomibuchi Y., Ngo K.X., Uyeda T.Q., and Wakabayashi T. : Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell 143 (2), 275-287, 2010.
  23. Noguchi T.Q., Gomibuchi Y., Murakami K., Ueno H., Hirose K., Wakabayashi T., and Uyeda T.Q. : Dominant negative mutant actins identified in flightless Drosophila can be classified into three classes. Journal of Biological Chemistry 285 (7), 4337-4437, 2010.
  24. Murakami K., Stewart M., Nozawa K., Tomii K., Kudou N., Igarashi N., Shirakihara Y., Wakatsuki S., Yasunaga T., and Wakabayashi T. : Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T. Proceedings of the National Academy of Sciences 105 (20), 7200-7205, 2008.
  25. Murakami K., Yumoto, F., Ohki S., Yasunaga T., Tanokura M., and Wakabayashi T. : Structural basis for calcium-regulated relaxation of striated muscles at interaction sites of troponin with actin and tropomyosin. Advances in Experimental Medicine and Biology 592, 71-86, 2007.
  26. Murakami K., Yumoto F., Ohki S., Yasunaga T., Tanokura M., and Wakabayashi T.: Structural basis for Ca2+-regulated muscle relaxation at interaction sites of troponin with actin and tropomyosin. Journal of Molecular Biology 352 (1), 178-201, 2005.