4ym5: Difference between revisions
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New page: '''Unreleased structure''' The entry 4ym5 is ON HOLD Authors: Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., ... |
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==Crystal structure of the human nucleosome containing 6-4PP (inside)== | |||
<StructureSection load='4ym5' size='340' side='right'caption='[[4ym5]], [[Resolution|resolution]] 4.00Å' 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]] 4.005Å</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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 4ym5" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: Iwai | *[[Histone 3D structures|Histone 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Hanaoka F]] | ||
[[Category: | [[Category: Hasegawa M]] | ||
[[Category: | [[Category: Horikoshi N]] | ||
[[Category: | [[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]] | |||
Latest revision as of 15:36, 8 November 2023
Crystal structure of the human nucleosome containing 6-4PP (inside)
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