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4ym5

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Revision as of 06:36, 12 June 2019

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

Structural highlights

4ym5 is a 10 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	4ym6
Gene:	HIST1H3A (HUMAN), HIST1H4A (HUMAN), HIST1H2AB (HUMAN), HIST1H2BJ (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] 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.^[4] ^[5] ^[6]

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ 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/4ym5"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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. 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 [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>
 </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">[[4ym6|4ym6]]</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]</span></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'>[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>
 == Function ==
@@ Line 18: / Line 20: @@
 </div>
 <div class="pdbe-citations 4ym5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone|Histone]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Hanaoka, F]]
 [[Category: Hasegawa, M]]

4ym5

From Proteopedia

Revision as of 06:36, 12 June 2019

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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