3mgp: Difference between revisions

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-{{Seed}}
-[[Image:3mgp.jpg|left|200px]]
-<!--
+==Binding of Cobalt ions to the Nucleosome Core Particle==
-The line below this paragraph, containing "STRUCTURE_3mgp", creates the "Structure Box" on the page.
+<StructureSection load='3mgp' size='340' side='right'caption='[[3mgp]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3mgp]] 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=3MGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MGP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.44&#8491;</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=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-{{STRUCTURE_3mgp|  PDB=3mgp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mgp OCA], [https://pdbe.org/3mgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mgp RCSB], [https://www.ebi.ac.uk/pdbsum/3mgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mgp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mg/3mgp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3mgp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co(2+) and Ni(2+) preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb(+) and Cs(+) are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn(2+) the aggressive coordination of Co(2+) and Ni(2+) to guanine bases is observed to induce a shift in histone-DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These 'softer' transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co(2+) and Ni(2+).
-===Binding of Cobalt ions to the Nucleosome Core Particle===
+Perturbations in nucleosome structure from heavy metal association.,Mohideen K, Muhammad R, Davey CA Nucleic Acids Res. 2010 May 21. PMID:20494975<ref>PMID:20494975</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3mgp" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20494975}}, adds the Publication Abstract to the page
+*[[Histone 3D structures|Histone 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20494975 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20494975}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-MGP 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=3MGP OCA].
-==Reference==
-<ref group="xtra">PMID:20494975</ref><references group="xtra"/>
 [[Category: Xenopus laevis]]
-[[Category: Davey, C A.]]
+[[Category: Davey CA]]
-[[Category: Mohideen, K.]]
+[[Category: Mohideen K]]
-[[Category: Muhammad, R.]]
+[[Category: Muhammad R]]
-[[Category: Protein-dna complex]]
-[[Category: Structural protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:42:23 2010''