5mC interactions in PDB entry 5CPK auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

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structural protein-DNA
X-ray (2.63 Å)
Nucleosome containing methylated sat2l DNA
List of 1 5mC-amino acid contact:
  1. I.5CM132: other-contacts is-WC-paired is-in-duplex [+]:TcG/cGA
direct SNAP output · DNAproDB 2.0
Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H.: (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5
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.

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List of 1 5mC-amino acid contact [summary · schematics · top · homepage · tutorial]

No. 1 I.5CM132: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:TcG/cGA