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Title: 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM
Authors: Chua, Eugene Yue Dao
Vogirala, Vinod Kumar
Inian, Oviya
Wong, Andrew See Weng
Nordenskiold, Lars
Plitzko, Juergen M.
Danev, Radostin
Sandin, Sara
Keywords: Nucleosome Core Particle
Issue Date: 2016
Source: Chua, E. Y. D., Vogirala, V. K., Inian, O., Wong, A. S. W., Nordenskiold, L., Plitzko, J. M., et al. (2016). 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM. Nucleic Acids Research, 44(17), 8013-8019.
Series/Report no.: Nucleic Acids Research
Abstract: The Volta phase plate is a recently developed electron cryo-microscopy (cryo-EM) device that enables contrast enhancement of biological samples. Here we have evaluated the potential of combining phase-plate imaging and single particle analysis to determine the structure of a small protein–DNA complex. To test the method, we made use of a 200 kDa Nucleosome Core Particle (NCP) reconstituted with 601 DNA for which a high-resolution X-ray crystal structure is known. We find that the phase plate provides a significant contrast enhancement that permits individual NCPs and DNA to be clearly identified in amorphous ice. The refined structure from 26,060 particles has an overall resolution of 3.9 Å and the density map exhibits structural features consistent with the estimated resolution, including clear density for amino acid side chains and DNA features such as the phosphate backbone. Our results demonstrate that phase-plate cryo-EM promises to become an important method to determine novel near-atomic resolution structures of small and challenging samples, such as nucleosomes in complex with nucleosome-binding factors.
ISSN: 0305-1048
DOI: 10.1093/nar/gkw708
Schools: School of Biological Sciences 
Research Centres: NTU Institute of Structural Biology 
Rights: © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Fulltext Permission: open
Fulltext Availability: With Fulltext
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