1pdq: Difference between revisions

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-{{Seed}}
-[[Image:1pdq.png|left|200px]]
-<!--
+==Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.==
-The line below this paragraph, containing "STRUCTURE_1pdq", creates the "Structure Box" on the page.
+<StructureSection load='1pdq' size='340' side='right'caption='[[1pdq]], [[Resolution|resolution]] 1.76&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'>[[1pdq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PDQ 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]] 1.76&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-{{STRUCTURE_1pdq|  PDB=1pdq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdq OCA], [https://pdbe.org/1pdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pdq RCSB], [https://www.ebi.ac.uk/pdbsum/1pdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pdq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PC_DROME PC_DROME] Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. Component of the PcG multiprotein PRC1 complex, a complex that acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-118', rendering chromatin heritably changed in its expressibility. Promotes locus-specific chromatin compaction.
+== 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/pd/1pdq_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=1pdq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+On the histone H3 tail, Lys 9 and Lys 27 are both methylation sites associated with epigenetic repression, and reside within a highly related sequence motif ARKS. Here we show that the chromodomain proteins Polycomb (Pc) and HP1 (heterochromatin protein 1) are highly discriminatory for binding to these sites in vivo and in vitro. In Drosophila S2 cells, and on polytene chromosomes, methyl-Lys 27 and Pc are both excluded from areas that are enriched in methyl-Lys 9 and HP1. Swapping of the chromodomain regions of Pc and HP1 is sufficient for switching the nuclear localization patterns of these factors, indicating a role for their chromodomains in both target site binding and discrimination. To better understand the molecular basis for the selection of methyl-lysine binding sites, we solved the 1.8 A structure of the Pc chromodomain in complex with a H3 peptide bearing trimethyl-Lys 27, and compared it with our previously determined structure of the HP1 chromodomain in complex with a H3 peptide bearing trimethyl-Lys 9. The Pc chromodomain distinguishes its methylation target on the H3 tail via an extended recognition groove that binds five additional residues preceding the ARKS motif.
-===Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.===
+Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains.,Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S Genes Dev. 2003 Aug 1;17(15):1870-81. PMID:12897054<ref>PMID:12897054</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pdq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12897054}}, adds the Publication Abstract to the page
+*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12897054 is the PubMed ID number.
+*[[Polycomb complex proteins 3D structures|Polycomb complex proteins 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12897054}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-PDQ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDQ OCA].
-==Reference==
-Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains., Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S, Genes Dev. 2003 Aug 1;17(15):1870-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12897054 12897054]
 [[Category: Drosophila melanogaster]]
-[[Category: Protein complex]]
+[[Category: Homo sapiens]]
-[[Category: Allis, C D.]]
+[[Category: Large Structures]]
-[[Category: Fischle, W.]]
+[[Category: Allis CD]]
-[[Category: Jacobs, S A.]]
+[[Category: Fischle W]]
-[[Category: Khorasanizadeh, S.]]
+[[Category: Jacobs SA]]
-[[Category: Kim, Y.]]
+[[Category: Khorasanizadeh S]]
-[[Category: Wang, Y.]]
+[[Category: Kim Y]]
-[[Category: Cation-pi]]
+[[Category: Wang Y]]
-[[Category: Chromo]]
-[[Category: Chromodomain]]
-[[Category: Histone h3]]
-[[Category: Lysine methylation]]
-[[Category: Methyllysine]]
-[[Category: Polycomb]]
-[[Category: Trimethyllysine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:30:21 2008''