This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
4ym6
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | ''' | + | ==Crystal structure of the human nucleosome containing 6-4PP (outside)== |
| + | <StructureSection load='4ym6' size='340' side='right' caption='[[4ym6]], [[Resolution|resolution]] 3.51Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4ym6]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YM6 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> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ym5|4ym5]]</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=4ym6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ym6 OCA], [http://pdbe.org/4ym6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ym6 RCSB], [http://www.ebi.ac.uk/pdbsum/4ym6 PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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<ref>PMID:26573481</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 4ym6" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Hanaoka, F]] | ||
| + | [[Category: Hasegawa, M]] | ||
| + | [[Category: Horikoshi, N]] | ||
| + | [[Category: Iwai, S]] | ||
| + | [[Category: Kagawa, W]] | ||
[[Category: Kurumizaka, H]] | [[Category: Kurumizaka, H]] | ||
| - | [[Category: | + | [[Category: Matsumoto, N]] |
| + | [[Category: Matsumoto, S]] | ||
[[Category: Osakabe, A]] | [[Category: Osakabe, A]] | ||
[[Category: Sugasawa, K]] | [[Category: Sugasawa, K]] | ||
| + | [[Category: Tachiwana, H]] | ||
| + | [[Category: Thoma, N H]] | ||
| + | [[Category: Toga, T]] | ||
[[Category: Yamamoto, J]] | [[Category: Yamamoto, J]] | ||
| - | [[Category: | + | [[Category: 6-4 photoproduct]] |
| - | [[Category: | + | [[Category: Dna binding]] |
| - | [[Category: | + | [[Category: Histone]] |
| - | [[Category: | + | [[Category: Nucleosome]] |
| - | [[Category: | + | [[Category: Structural protein-dna complex]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Revision as of 16:09, 2 December 2015
Crystal structure of the human nucleosome containing 6-4PP (outside)
| |||||||||||
