1m7u: Difference between revisions

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 ==Crystal structure of a novel DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast==
-<StructureSection load='1m7u' size='340' side='right' caption='[[1m7u]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1m7u' size='340' side='right'caption='[[1m7u]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1m7u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7U FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m6u|1m6u]]</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ndt80 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1m7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7u OCA], [https://pdbe.org/1m7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7u RCSB], [https://www.ebi.ac.uk/pdbsum/1m7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7u ProSAT]</span></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=1m7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7u OCA], [http://pdbe.org/1m7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m7u RCSB], [http://www.ebi.ac.uk/pdbsum/1m7u PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NDT80_YEAST NDT80_YEAST]] Transcription factor required for successful completion of meiosis and spore formation. Gets activated after completion of meiotic recombination at the end of prophase I. Recognizes and binds to the middle sporulation element (MSE) 5'-C[AG]CAAA[AT]-3' in the promoter region of stage-specific genes that are required for progression through meiosis and sporulation. Competes for binding to MSE with the transcriptional repressor SUM1, which represses middle sporulation-specific genes during mitosis and early sporulation.<ref>PMID:8524222</ref> <ref>PMID:9660952</ref> <ref>PMID:9742092</ref> <ref>PMID:12832469</ref>
+[https://www.uniprot.org/uniprot/NDT80_YEAST NDT80_YEAST] Transcription factor required for successful completion of meiosis and spore formation. Gets activated after completion of meiotic recombination at the end of prophase I. Recognizes and binds to the middle sporulation element (MSE) 5'-C[AG]CAAA[AT]-3' in the promoter region of stage-specific genes that are required for progression through meiosis and sporulation. Competes for binding to MSE with the transcriptional repressor SUM1, which represses middle sporulation-specific genes during mitosis and early sporulation.<ref>PMID:8524222</ref> <ref>PMID:9660952</ref> <ref>PMID:9742092</ref> <ref>PMID:12832469</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/m7/1m7u_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m7/1m7u_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1m7u ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ndt80 is a transcriptional activator required for meiosis in the yeast Saccharomyces cerevisiae. Here, we report the crystal structure at 2.3 A resolution of the DNA-binding domain of Ndt80 experimentally phased by using the anomalous and isomorphous signal from a single ordered Se atom per molecule of 272-aa residues. The structure reveals a single approximately 32-kDa domain with a distinct fold comprising a beta-sandwich core elaborated with seven additional beta-sheets and three short alpha-helices. Inspired by the structure, we have performed a mutational analysis and defined a DNA-binding motif in this domain. The DNA-binding domain of Ndt80 is homologous to a number of proteins from higher eukaryotes, and the residues that we have shown are required for DNA binding by Ndt80 are highly conserved among this group of proteins. These results suggest that Ndt80 is the defining member of a previously uncharacterized family of transcription factors, including the human protein (C11orf9), which has been shown to be highly expressed in invasive or metastatic tumor cells.
-Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast.,Montano SP, Cote ML, Fingerman I, Pierce M, Vershon AK, Georgiadis MM Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14041-6. Epub 2002 Oct 16. PMID:12384578<ref>PMID:12384578</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1m7u" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Cote, M L]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Fingerman, I]]
+[[Category: Cote ML]]
-[[Category: Georgiadis, M M]]
+[[Category: Fingerman I]]
-[[Category: Montano, S P]]
+[[Category: Georgiadis MM]]
-[[Category: Pierce, M]]
+[[Category: Montano SP]]
-[[Category: Vershon, A K]]
+[[Category: Pierce M]]
-[[Category: Dna-binding]]
+[[Category: Vershon AK]]
-[[Category: Meiosis]]
-[[Category: Transcription activator]]
-[[Category: Yeast protein]]