3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

Nucleic Acids Research

Volumn 44, Issue 17, 2016, Pages 8013-8019

  Chua, Eugene Y D ^a   Vogirala, Vinod K ^a   Inian, Oviya ^a   Wong, Andrew S W ^b   Nordenskiöld, Lars ^a   Plitzko, Juergen M ^c   Danev, Radostin ^c   Sandin, Sara ^a,b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DNA; NUCLEOSOME;

ARTICLE; BINDING KINETICS; CHROMATIN; COMPLEX FORMATION; CONTRAST ENHANCEMENT; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DNA PROTEIN COMPLEX; NUCLEOSOME; NUCLEOSOME CORE PARTICLE; PRIORITY JOURNAL; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; ANIMAL; PROCEDURES; ULTRASTRUCTURE; XENOPUS LAEVIS;

ANIMALS; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; DNA; NUCLEOSOMES; XENOPUS LAEVIS;

EID: 84991368997     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw708     Document Type: Article

References (32)

1. Bai, X.C., McMullan, G. and Scheres, S.H. (2015) How cryo-EM is revolutionizing structural biology. Trends Biochem. Sci., 40, 49-57.
2. Cheng, Y., Grigorieff, N., Penczek, P.A. and Walz, T. (2015) A primer to single-particle cryo-electron microscopy. Cell, 161, 438-449.
3. Nogales, E. and Scheres, S.H. (2015) Cryo-EM: A unique tool for the visualization of macromolecular complexity. Mol. Cell 58, 677-689.
4. Henderson, R. (1995) The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys., 28, 171-193.
5. Baker, L.A. and Rubinstein, J.L. (2010) Radiation damage in electron cryomicroscopy. Methods Enzymol., 481, 371-388.
6. Glaeser, R.M. (2013) Invited review article: Methods for imaging weak-phase objects in electron microscopy. Rev. Sci. Instrum., 84, 111101.
7. Khoshouei, M., Radjainia, M., Phillips, A.J., Gerrard, J.A., Mitra, A.K., Plitzko, J.M., Baumeister, W. and Danev, R. (2016) Volta phase plate cryo-EM of the small protein complex Prx3. Nat. Commun., 7, 10534.
8. Kornberg, R.D. (1974) Chromatin structure: A repeating unit of histones and DNA. Science, 184, 868-871.
9. Finch, J.T., Lutter, L.C., Rhodes, D., Brown, R.S., Rushton, B., Levitt, M. and Klug, A. (1977) Structure of nucleosome core particles of chromatin. Nature, 269, 29-36.
10. Olins, A.L. and Olins, D.E. (1974) Spheroid chromatin units (v bodies). Science, 183, 330-332.
11. Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D. and Klug, A. (1984) Structure of the nucleosome core particle at 7 Å resolution. Nature, 311, 532-537.
12. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260.
13. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. and Richmond, T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol., 319, 1097-113.
14. Danev, R., Buijsse, B., Khoshouei, M., Plitzko, J.M. and Baumeister, W. (2014) Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. U.S.A., 111, 15635-15640.
15. Dyer, P.N., Edayathumangalam, R.S., White, C.L., Bao, Y., Chakravarthy, S., Muthurajan, U. M. and Luger, K. (2004) Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol., 375, 23-44.
16. Mastronarde, D.N. (2005) Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol., 152, 36-51.
17. Kremer, J.R., Mastronarde, D.N. and McIntosh, J.R. (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol., 116, 71-76.
18. Grant, T. and Grigorieff, N. (2015) Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. Elife, 4, e06980.
19. Ludtke, S.J., Baldwin, P.R. and Chiu, W. (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol., 128, 82-97.
20. Scheres, S.H. (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol., 180, 519-530.
21. Kucukelbir, A., Sigworth, F.J. and Tagare, H.D. (2014) Quantifying the local resolution of cryo-EM density maps. Nat. Methods, 11, 63-65.
22. Schneider, C.A., Rasband, W.S. and Eliceiri, K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat. Methods, 9, 671-675.
23. Goddard, T.D., Huang, C.C. and Ferrin, T.E. (2007) Visualizing density maps with UCSF Chimera. J. Struct. Biol., 157, 281-287.
24. Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J. and Grosse-Kunstleve, R.W. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr., 66, 213-221.
25. Lowary, P.T. and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol., 276, 19-42.
26. Danev, R. and Baumeister, W.(2016) Cryo-EM single particle analysis with the Volta phase plate. Elife, 5, e13046.
27. Vasudevan, D., Chua, E.Y. and Davey, C.A. (2010) Crystal structures of nucleosome core particles containing the '601' strong positioning sequence. J. Mol. Biol., 403, 1-10.
28. Yamada, K., Frouws, T.D., Angst, B., Fitzgerald, D.J., De Luca, C., Schimmele, K., Sargent, D.F. and Richmond, T.J. (2011) Structure and mechanism of the chromatin remodelling factor ISW1a. Nature, 472, 448-453.
29. Chaban, Y., Ezeokonkwo, C., Chung, W.H., Zhang, F., Kornberg, R.D., Maier-Davis, B., Lorch, Y. and Asturias, F.J. (2008) Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat. Struct. Mol. Biol., 15, 1272-1277.
30. Song, F., Chen, P., Sun, D., Wang, M., Dong, L., Liang, D., Xu, R.M., Zhu, P. and Li, G. (2014) Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science 344, 376-380.
31. Maskell, D.P., Renault, L., Serrao, E., Lesbats, P., Matadeen, R., Hare, S., Lindemann, D., Engelman, A.N., Costa, A. and Cherepanov, P. (2015) Structural basis for retroviral integration into nucleosomes. Nature, 523, 366-369.
32. McGinty, R.K. and Tan, S. (2016) Recognition of the nucleosome by chromatin factors and enzymes. Curr. Opin. Struct. Biol., 37, 54-61.