3424–3434 Nucleic Acids Research, 2005, Vol. 33, No. 10 doi:10.1093/nar/gki663 Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle Yasuo Tsunaka, Naoko Kajimura, Shin-ichi Tate and Kosuke Morikawa* Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan Received March 23, 2005; Revised May 16, 2005; Accepted May 30, 2005 ABSTRACT Gene expression in eukaryotes depends upon posi- tioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A˚ crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location 5.0 to 2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA–DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local altera- tion of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment. INTRODUCTION DNA in eukaryotic nuclei is organized in a hierarchical scheme of folding and compaction into protein–DNA assem- blies, collectively called chromatin (1–3). Genetic processes, such as transcription and replication, depend on chromatin structures, which affect the DNA transaction activity (4–9). Therefore, chromatin structures play a central role in the regu- lation of the gene expression processes in nuclei. At the lowest level of organization, two copies of each of the four histone proteins, H2A, H2B, H3 and H4, are assembled into an octamer, which is wrapped by two tight superhelical turns of 145–147 bp of DNA to form a nucleosome core particle (NCP) (10). In higher eukaryotes, the addition of the linker histone H1 to the linker DNA forms nucleosomes, correspond- ing to the basic repeating unit of chromatin. High-resolution structures of NCPs from different organ- isms, such as Xenopus laevis (11,12), chicken (13) and yeast (14), are already available. The DNA-dependent divalent cation binding in an NCP of X.laevis (Xla-NCP) was invest- igated in detail (15). Recently, the structural geometry of the nucleosomal DNA has been evaluated in the Xla-NCP structure at 1.9 s resolution (16). The overall NCP structures are very similar to each other among the available ones. The histone sequences are highly conserved among eukaryotic organisms (17). However, the crystal structure of a yeast NCP revealed the signiﬁcant differences in the internucleosome interactions, as compared with those of other NCPs (14). This fact prompts us to investigate the details in the human NCP structure, which may allow us to clarify the differences from other NCPs. Although the organization of DNA into nucleosomes, which is essentially ubiquitous among genomes, generally results in gene expression control in a repressive manner, its certain modes also contribute to gene-speciﬁc transcription. This suggests that nucleosome positioning in gene promoters is crucial for transcriptional regulation in vivo (18–21). The question, therefore, arises as to how the chromatin structure, leading to DNA compaction, permits the site-speciﬁc access to regulatory factors and the more extensive exposure to transcription proteins. To answer this question, we need the detailed conformational view of the nucleosomal DNA, which could contribute toward an understanding of basic chromatin properties, such as nucleosome positioning and mobility. Here, we report the 2.5 s resolution crystal structure of human NCP, which facilitates a comparison with those of other NCPs determined so far. The overall structures of all of these NCPs are very similar, in agreement with the minor *To whom correspondence should be addressed. Tel: +81 6 6872 8211; Fax: +81 6 6872 8210; Email: morikawa@beri.or.jp The Author 2005. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. 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