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| | <StructureSection load='4ym5' size='340' side='right'caption='[[4ym5]], [[Resolution|resolution]] 4.00Å' scene=''> | | <StructureSection load='4ym5' size='340' side='right'caption='[[4ym5]], [[Resolution|resolution]] 4.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ym5]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YM5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ym5]] 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=4YM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YM5 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=T64:(6-4)PHOTOPRODUCT'>T64</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]] 4.005Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ym6|4ym6]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T64:(6-4)PHOTOPRODUCT'>T64</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HIST1H3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4ym5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ym5 OCA], [https://pdbe.org/4ym5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ym5 RCSB], [https://www.ebi.ac.uk/pdbsum/4ym5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ym5 ProSAT]</span></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=4ym5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ym5 OCA], [http://pdbe.org/4ym5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ym5 RCSB], [http://www.ebi.ac.uk/pdbsum/4ym5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ym5 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hanaoka, F]] | + | [[Category: Hanaoka F]] |
| - | [[Category: Hasegawa, M]] | + | [[Category: Hasegawa M]] |
| - | [[Category: Horikoshi, N]] | + | [[Category: Horikoshi N]] |
| - | [[Category: Iwai, S]] | + | [[Category: Iwai S]] |
| - | [[Category: Kagawa, W]] | + | [[Category: Kagawa W]] |
| - | [[Category: Kurumizaka, H]] | + | [[Category: Kurumizaka H]] |
| - | [[Category: Matsumoto, N]] | + | [[Category: Matsumoto N]] |
| - | [[Category: Matsumoto, S]] | + | [[Category: Matsumoto S]] |
| - | [[Category: Osakabe, A]] | + | [[Category: Osakabe A]] |
| - | [[Category: Sugasawa, K]] | + | [[Category: Sugasawa K]] |
| - | [[Category: Tachiwana, H]] | + | [[Category: Tachiwana H]] |
| - | [[Category: Thoma, N H]] | + | [[Category: Thoma NH]] |
| - | [[Category: Toga, T]] | + | [[Category: Toga T]] |
| - | [[Category: Yamamoto, J]] | + | [[Category: Yamamoto J]] |
| - | [[Category: Dna binding]]
| + | |
| - | [[Category: Histone]]
| + | |
| - | [[Category: Nucleosome]]
| + | |
| - | [[Category: Structural protein-dna complex]]
| + | |
| Structural highlights
Function
H31_HUMAN
Publication Abstract from PubMed
UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6-4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6-4PPs in these rotational positions, and found that the 6-4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6-4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin.
Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome.,Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka H Sci Rep. 2015 Nov 17;5:16330. doi: 10.1038/srep16330. PMID:26573481[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka H. Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome. Sci Rep. 2015 Nov 17;5:16330. doi: 10.1038/srep16330. PMID:26573481 doi:http://dx.doi.org/10.1038/srep16330
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