3mea: Difference between revisions

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-[[Image:3mea.png|left|200px]]
-<!--
+==Crystal structure of the SGF29 in complex with H3K4me3==
-The line below this paragraph, containing "STRUCTURE_3mea", creates the "Structure Box" on the page.
+<StructureSection load='3mea' size='340' side='right'caption='[[3mea]], [[Resolution|resolution]] 1.26&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'>[[3mea]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MEA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MEA 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]] 1.26&#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_3mea|  PDB=3mea  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mea OCA], [https://pdbe.org/3mea PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mea RCSB], [https://www.ebi.ac.uk/pdbsum/3mea PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mea ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SGF29_HUMAN SGF29_HUMAN] Involved in transcriptional regulation, through association with histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes. Specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3). In the SAGA-type complexes, required to recruit complexes to H3K4me. May be involved in MYC-mediated oncogenic transformation.<ref>PMID:19103755</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/me/3mea_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=3mea ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.
-===Crystal structure of the SGF29 in complex with H3K4me3===
+Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation.,Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO, Fleharty BE, Paulson A, Allali-Hassani A, Zhou JQ, Mer G, Grant PA, Workman JL, Zang J, Min J EMBO J. 2011 Jun 17. doi: 10.1038/emboj.2011.193. PMID:21685874<ref>PMID:21685874</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3mea" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21685874}}, adds the Publication Abstract to the page
+*[[SAGA-associated factor|SAGA-associated factor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21685874 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21685874}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3mea]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MEA OCA].
-==Reference==
-<ref group="xtra">PMID:021685874</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Large Structures]]
-[[Category: Bian, C.]]
+[[Category: Xenopus laevis]]
-[[Category: Bochkarev, A.]]
+[[Category: Arrowsmith CH]]
-[[Category: Bountra, C.]]
+[[Category: Bian C]]
-[[Category: Edwards, A M.]]
+[[Category: Bochkarev A]]
-[[Category: MacKenzie, F.]]
+[[Category: Bountra C]]
-[[Category: Min, J.]]
+[[Category: Edwards AM]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: MacKenzie F]]
-[[Category: Tempel, W.]]
+[[Category: Min J]]
-[[Category: Weigelt, J.]]
+[[Category: Tempel W]]
-[[Category: Xu, C.]]
+[[Category: Weigelt J]]
-[[Category: Chromosomal protein]]
+[[Category: Xu C]]
-[[Category: Dna-binding]]
-[[Category: Nucleosome core]]
-[[Category: Nucleus]]
-[[Category: Sgc]]
-[[Category: Structural genomics consortium]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]