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| | ==Nucleosome containing methylated Sat2R DNA== | | ==Nucleosome containing methylated Sat2R DNA== |
| - | <StructureSection load='5cpj' size='340' side='right' caption='[[5cpj]], [[Resolution|resolution]] 3.15Å' scene=''> | + | <StructureSection load='5cpj' size='340' side='right'caption='[[5cpj]], [[Resolution|resolution]] 3.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CPJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CPJ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5cpi|5cpi]], [[5cpk|5cpk]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [http://pdbe.org/5cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [http://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [https://pdbe.org/5cpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [https://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> | + | [https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Histone|Histone]] | + | *[[Histone 3D structures|Histone 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adachi, F]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Arimura, Y]] | + | [[Category: Large Structures]] |
| - | [[Category: Kurumizaka, H]] | + | [[Category: Adachi F]] |
| - | [[Category: Maehara, K]] | + | [[Category: Arimura Y]] |
| - | [[Category: Ohkawa, Y]]
| + | [[Category: Kurumizaka H]] |
| - | [[Category: Osakabe, A]] | + | [[Category: Maehara K]] |
| - | [[Category: Structural protein-dna complex]] | + | [[Category: Ohkawa Y]] |
| - | [[Category: Chromatin formation]] | + | [[Category: Osakabe A]] |
| - | [[Category: Dna binding]] | + | |
| - | [[Category: Dna methylation]]
| + | |
| - | [[Category: Histone fold]]
| + | |
| - | [[Category: Nucleosome]]
| + | |
| - | [[Category: Nucleus]]
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| Structural highlights
Function
H31_HUMAN
Publication Abstract from PubMed
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.
Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.,Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H Open Biol. 2015 Oct;5(10). pii: 150128. doi: 10.1098/rsob.150128. PMID:26446621[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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 Biol. 2015 Oct;5(10). pii: 150128. doi: 10.1098/rsob.150128. PMID:26446621 doi:http://dx.doi.org/10.1098/rsob.150128
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