5jrg: Difference between revisions

Revision as of 11:35, 17 June 2020

Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)

Structural highlights

5jrg is a 10 chain structure with sequence from [1] and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CL, MN
NonStd Res:	3DR
Gene:	HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ (HUMAN), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 (HUMAN), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA (HUMAN), HIST1H2BJ, H2BFR (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

Huge amounts (>10,000/day) of apurinic/apyrimidinic (AP) sites are produced in genomes, but their structures in chromatin remain undetermined. We determined the crystal structure of the nucleosome containing AP-site analogs at two symmetric sites, which revealed structural polymorphism: one forms an inchworm configuration without an empty space at the AP site, and the other forms a B-form-like structure with an empty space and the orphan base. This unexpected inchworm configuration of the AP site is important to understand the AP DNA repair mechanism, because it may not be recognized by the major AP-binding protein, APE1, during the base excision repair process.

Polymorphism of apyrimidinic DNA structures in the nucleosome.,Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783. PMID:28139742^[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, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H. Polymorphism of apyrimidinic DNA structures in the nucleosome. Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783. PMID:28139742 doi:https://dx.doi.org/10.1038/srep41783

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[3] 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

[4] 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

[5] 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

[6] 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

[7] Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H. Polymorphism of apyrimidinic DNA structures in the nucleosome. Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783. PMID:28139742 doi:https://dx.doi.org/10.1038/srep41783

[1]

[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)==
-<StructureSection load='5jrg' size='340' side='right' caption='[[5jrg]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='5jrg' size='340' side='right'caption='[[5jrg]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jrg]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JRG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jrg]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JRG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></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=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [http://pdbe.org/5jrg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [http://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BJ, H2BFR ([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://proteopedia.org/fgij/fg.htm?mol=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [http://pdbe.org/5jrg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [http://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5jrg" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone 3D structures|Histone 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Arimura, Y]]
 [[Category: Horikoshi, N]]

5jrg: Difference between revisions

Revision as of 11:35, 17 June 2020

Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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