2nzd

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{{Seed}}
 
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[[Image:2nzd.png|left|200px]]
 
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==Nucleosome core particle containing 145 bp of DNA==
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The line below this paragraph, containing "STRUCTURE_2nzd", creates the "Structure Box" on the page.
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<StructureSection load='2nzd' size='340' side='right'caption='[[2nzd]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2nzd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NZD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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{{STRUCTURE_2nzd| PDB=2nzd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nzd OCA], [https://pdbe.org/2nzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nzd RCSB], [https://www.ebi.ac.uk/pdbsum/2nzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nzd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/H32_XENLA H32_XENLA] 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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nz/2nzd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nzd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA stretching in chromatin may facilitate its compaction and influence site recognition by nuclear factors. In vivo, stretching has been estimated to occur at the equivalent of one to two base-pairs (bp) per nucleosome. We have determined the crystal structure of a nucleosome core particle containing 145 bp of DNA (NCP145). Compared to the structure with 147 bp, the NCP145 displays two incidences of stretching one to two double-helical turns from the particle dyad axis. The stretching illustrates clearly a mechanism for shifting DNA position by displacement of a single base-pair while maintaining nearly identical histone-DNA interactions. Increased DNA twist localized to a short section between adjacent histone-DNA binding sites advances the rotational setting, while a translational component involves DNA kinking at a flanking region that initiates elongation by unstacking bases. Furthermore, one stretched region of the NCP145 displays an extraordinary 55 degrees kink into the minor groove situated 1.5 double-helical turns from the particle dyad axis, a hot spot for gene insertion by HIV-integrase, which prefers highly distorted substrate. This suggests that nucleosome position and context within chromatin could promote extreme DNA kinking that may influence genomic processes.
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===Nucleosome core particle containing 145 bp of DNA===
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DNA stretching and extreme kinking in the nucleosome core.,Ong MS, Richmond TJ, Davey CA J Mol Biol. 2007 May 11;368(4):1067-74. Epub 2007 Mar 2. PMID:17379244<ref>PMID:17379244</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2nzd" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17379244}}, adds the Publication Abstract to the page
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*[[Histone 3D structures|Histone 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17379244 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17379244}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2NZD is a 10 chains structure of sequences from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NZD OCA].
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==Reference==
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<ref group="xtra">PMID:17379244</ref><references group="xtra"/>
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[[Category: Xenopus laevis]]
[[Category: Xenopus laevis]]
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[[Category: Davey, C A.]]
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[[Category: Davey CA]]
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[[Category: Ong, M S.]]
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[[Category: Ong MS]]
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[[Category: Richmond, T J.]]
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[[Category: Richmond TJ]]
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[[Category: Chromatin]]
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[[Category: Dna kinking]]
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[[Category: Dna stretching]]
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[[Category: Double-helix]]
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[[Category: Histone]]
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[[Category: Nucleosome]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:55:30 2009''
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Current revision

Nucleosome core particle containing 145 bp of DNA

PDB ID 2nzd

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