5CPK
Nucleosome containing methylated Sat2L DNA
Summary for 5CPK
| Entry DOI | 10.2210/pdb5cpk/pdb |
| Related | 5CPI 5CPJ |
| Descriptor | Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total) |
| Functional Keywords | histone fold, dna binding, nucleus, nucleosome, chromatin formation, dna methylation, structural protein-dna complex, structural protein/dna |
| Biological source | Homo sapiens (Human) More |
| Total number of polymer chains | 10 |
| Total formula weight | 201750.66 |
| Authors | Osakabe, A.,Arimura, Y.,Adachi, F.,Maehara, K.,Ohkawa, Y.,Kurumizaka, H. (deposition date: 2015-07-21, release date: 2015-10-28, Last modification date: 2023-11-08) |
| Primary citation | Osakabe, A.,Adachi, F.,Arimura, Y.,Maehara, K.,Ohkawa, Y.,Kurumizaka, H. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5:-, 2015 Cited by PubMed Abstract: DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells. PubMed: 26446621DOI: 10.1098/rsob.150128 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.632 Å) |
Structure validation
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