3lel

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{{Seed}}
 
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[[Image:3lel.jpg|left|200px]]
 
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==Structural Insight into the Sequence-Dependence of Nucleosome Positioning==
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The line below this paragraph, containing "STRUCTURE_3lel", creates the "Structure Box" on the page.
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<StructureSection load='3lel' size='340' side='right'caption='[[3lel]], [[Resolution|resolution]] 2.95&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'>[[3lel]] is a 20 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=3LEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEL 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]] 2.95&#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_3lel| PDB=3lel | 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=3lel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lel OCA], [https://pdbe.org/3lel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lel RCSB], [https://www.ebi.ac.uk/pdbsum/3lel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lel 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/le/3lel_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=3lel 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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Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.
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===Structural Insight into the Sequence-Dependence of Nucleosome Positioning===
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Structural insight into the sequence dependence of nucleosome positioning.,Wu B, Mohideen K, Vasudevan D, Davey CA Structure. 2010 Mar 14;18(4):528-36. PMID:20399189<ref>PMID:20399189</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 3lel" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20399189}}, 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 20399189 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20399189}}
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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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3LEL is a 20 chains structure with 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=3LEL OCA].
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==Reference==
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<ref group="xtra">PMID:20399189</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: Vasudevan, D.]]
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[[Category: Vasudevan D]]
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[[Category: Wu, B.]]
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[[Category: Wu B]]
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[[Category: Acetylation]]
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[[Category: Chromatin]]
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[[Category: Chromosomal protein]]
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[[Category: Dna flexibility]]
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[[Category: Dna-binding]]
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[[Category: Methylation]]
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[[Category: Nucleosome]]
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[[Category: Nucleosome core]]
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[[Category: Nucleosome positioning]]
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[[Category: Nucleus]]
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[[Category: Structural protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:30:47 2010''
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Current revision

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

PDB ID 3lel

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