3o70: Difference between revisions

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 ==PHD-type zinc finger of human PHD finger protein 13==
-<StructureSection load='3o70' size='340' side='right' caption='[[3o70]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3o70' size='340' side='right'caption='[[3o70]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o70]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O70 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o70]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O70 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHF13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3o70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o70 OCA], [http://pdbe.org/3o70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o70 RCSB], [http://www.ebi.ac.uk/pdbsum/3o70 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o70 OCA], [https://pdbe.org/3o70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o70 RCSB], [https://www.ebi.ac.uk/pdbsum/3o70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o70 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHF13_HUMAN PHF13_HUMAN]] Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.<ref>PMID:19638409</ref>
+[https://www.uniprot.org/uniprot/PHF13_HUMAN PHF13_HUMAN] Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.<ref>PMID:19638409</ref>
 == 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/o7/3o70_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/3o70_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=3o70 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.
-PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3.,Chung HR, Xu C, Fuchs A, Mund A, Lange M, Staege H, Schubert T, Bian C, Dunkel I, Eberharter A, Regnard C, Klinker H, Meierhofer D, Cozzuto L, Winterpacht A, Di Croce L, Min J, Will H, Kinkley S Elife. 2016 May 25;5. pii: e10607. doi: 10.7554/eLife.10607. PMID:27223324<ref>PMID:27223324</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3o70" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H]]
+[[Category: Large Structures]]
-[[Category: Bian, C B]]
+[[Category: Arrowsmith CH]]
-[[Category: Bochkarev, A]]
+[[Category: Bian CB]]
-[[Category: Bountra, C]]
+[[Category: Bochkarev A]]
-[[Category: Edwards, A M]]
+[[Category: Bountra C]]
-[[Category: Kania, J]]
+[[Category: Edwards AM]]
-[[Category: Lam, R]]
+[[Category: Kania J]]
-[[Category: Min, J]]
+[[Category: Lam R]]
-[[Category: Structural genomic]]
+[[Category: Min J]]
-[[Category: Weigelt, J]]
+[[Category: Weigelt J]]
-[[Category: Xu, C]]
+[[Category: Xu C]]
-[[Category: Phd-type zinc finger]]
-[[Category: Phf13]]
-[[Category: Protein binding]]
-[[Category: Sgc]]
-[[Category: Zinc ion binding]]