6ugm: Difference between revisions

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 <SX load='6ugm' size='340' side='right' viewer='molstar' caption='[[6ugm]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ugm]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Candida_sphaerica Candida sphaerica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UGM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UGM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ugm]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140], [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UGM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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">Electron Microscopy, [[Resolution|Resolution]] 3.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hist1h3g, H3l ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog]), KLLA0_A08800g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica]), KLLA0_D07260g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica]), KLLA0_C10945g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica]), KLLA0_E03521g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica]), hist1h2aj, LOC494591, XELAEV_18003602mg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog]), XELAEV_18032686mg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog]), KLLA0_E24487g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica]), SET1, KLLA0F24134g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=6ugm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ugm OCA], [https://pdbe.org/6ugm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ugm RCSB], [https://www.ebi.ac.uk/pdbsum/6ugm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ugm ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ugm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ugm OCA], [http://pdbe.org/6ugm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ugm RCSB], [http://www.ebi.ac.uk/pdbsum/6ugm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ugm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SET1_KLULA SET1_KLULA]] Catalytic component of the COMPASS (Set1C) complex that specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. [[http://www.uniprot.org/uniprot/H4_XENLA H4_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. [[http://www.uniprot.org/uniprot/H2B11_XENLA H2B11_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.
+[https://www.uniprot.org/uniprot/Q92133_XENLA Q92133_XENLA]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that autoinhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By delineating the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
-Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS.,Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N Mol Cell. 2019 Oct 29. pii: S1097-2765(19)30791-9. doi:, 10.1016/j.molcel.2019.10.013. PMID:31733991<ref>PMID:31733991</ref>
+==See Also==
+*[[Histone 3D structures|Histone 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
-</div>
-<div class="pdbe-citations 6ugm" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: African clawed frog]]
+[[Category: Kluyveromyces lactis NRRL Y-1140]]
-[[Category: Candida sphaerica]]
-[[Category: Histone-lysine N-methyltransferase]]
 [[Category: Large Structures]]
-[[Category: Hsu, P L]]
+[[Category: Synthetic construct]]
-[[Category: Shi, H]]
+[[Category: Xenopus laevis]]
-[[Category: Zheng, N]]
+[[Category: Hsu PL]]
-[[Category: Chromatin]]
+[[Category: Shi H]]
-[[Category: Complex]]
+[[Category: Zheng N]]
-[[Category: Epigenetic]]
-[[Category: Methyltransferase]]
-[[Category: Nucleosome]]
-[[Category: Transferase-structural protein-dna complex]]