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4ym6

From Proteopedia

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Crystal structure of the human nucleosome containing 6-4PP (outside)

Structural highlights

4ym6 is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.514Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ym6"

@@ Line 3: / Line 3: @@
 <StructureSection load='4ym6' size='340' side='right'caption='[[4ym6]], [[Resolution|resolution]] 3.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ym6]] 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=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>
+<table><tr><td colspan='2'>[[4ym6]] 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=4YM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.514&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ym5|4ym5]]</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=4ym6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ym6 OCA], [https://pdbe.org/4ym6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ym6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ym6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ym6 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=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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ym6 ProSAT]</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>
+[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Histone|Histone]]
+*[[Histone 3D structures|Histone 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[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: 6-4 photoproduct]]
-[[Category: Dna binding]]
-[[Category: Histone]]
-[[Category: Nucleosome]]
-[[Category: Structural protein-dna complex]]

4ym6

From Proteopedia

Current revision

Crystal structure of the human nucleosome containing 6-4PP (outside)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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