3lja

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{{Seed}}
 
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[[Image:3lja.jpg|left|200px]]
 
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==Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome==
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The line below this paragraph, containing "STRUCTURE_3lja", creates the "Structure Box" on the page.
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<StructureSection load='3lja' size='340' side='right'caption='[[3lja]], [[Resolution|resolution]] 2.75&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'>[[3lja]] 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=3LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LJA 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]] 2.75&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3lja| PDB=3lja | 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=3lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lja OCA], [https://pdbe.org/3lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lja RCSB], [https://www.ebi.ac.uk/pdbsum/3lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lja 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/lj/3lja_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=3lja 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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Divalent metals associate with DNA in a site-selective manner, which can influence nucleosome positioning, mobility, compaction, and recognition by nuclear factors. We previously characterized divalent metal binding in the nucleosome core using hard (short-wavelength) X-rays allowing high-resolution crystallographic determination of the strongest affinity sites, which revealed that Mn(2+) associates with the DNA major groove in a sequence- and conformation-dependent manner. In this study, we obtained diffraction data with soft X-rays at the Mn(2+) absorption edge for a core particle crystal in the presence of 10 mM MnSO(4), mimicking prevailing Mg(2+) concentration in the nucleus. This provides an exceptional view of counterion binding in the nucleosome through identification of 45 divalent metal binding sites. In addition to that at the well-characterized major interparticle interface, only one other histone-divalent metal binding site is found, which corresponds to a symmetry-related counterpart on the 'free' H2B alpha1 helix C-terminus. This emphasizes the importance of the alpha-helix dipole in ion binding and suggests that the H2B motif may serve as a nucleation site in nucleosome compaction. The 43 sites associated with the DNA are characterized by (1) high-affinity direct coordination at the most electrostatically favorable major groove locations, (2) metal hydrate binding to the major groove, (3) direct coordination to phosphate groups at sites of high charge density, (4) metal hydrate binding in the minor groove, or (5) metal hydrate-divalent anion pairing. Metal hydrates are found within the minor groove only at locations displaying a narrow range of high-intermediate width and to which histone N-terminal tails are not associated or proximal. This indicates that divalent metals and histone tails can both collaborate and compete in minor groove association, which sheds light on nucleosome solubility and chromatin compaction behavior.
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===Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome===
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Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome.,Wu B, Davey CA J Mol Biol. 2010 May 21;398(5):633-40. Epub 2010 Mar 27. PMID:20350553<ref>PMID:20350553</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 3lja" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20350553}}, 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 20350553 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20350553}}
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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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3LJA is a 10 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=3LJA OCA].
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==Reference==
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<ref group="xtra">PMID:20350553</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: Wu, B.]]
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[[Category: Wu B]]
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[[Category: Acetylation]]
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[[Category: Cation binding]]
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[[Category: Chromosomal protein]]
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[[Category: Compaction]]
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[[Category: Counterion]]
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[[Category: Divalent metal]]
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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: 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 Wed Apr 14 09:38:10 2010''
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Current revision

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

PDB ID 3lja

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