View source for 4ym5


==Crystal structure of the human nucleosome containing 6-4PP (inside)==
<StructureSection load='4ym5' size='340' side='right'caption='[[4ym5]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.005&#8491;</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='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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN] 
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4ym5" style="background-color:#fffaf0;"></div>

==See Also==
*[[Histone 3D structures|Histone 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Hanaoka F]]
[[Category: Hasegawa M]]
[[Category: Horikoshi N]]
[[Category: Iwai S]]
[[Category: Kagawa W]]
[[Category: Kurumizaka H]]
[[Category: Matsumoto N]]
[[Category: Matsumoto S]]
[[Category: Osakabe A]]
[[Category: Sugasawa K]]
[[Category: Tachiwana H]]
[[Category: Thoma NH]]
[[Category: Toga T]]
[[Category: Yamamoto J]]