2gcc: Difference between revisions
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==SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED MEAN STRUCTURE== | ==SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED MEAN STRUCTURE== | ||
<StructureSection load='2gcc' size='340' side='right' caption='[[2gcc]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | <StructureSection load='2gcc' size='340' side='right' caption='[[2gcc]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | ||
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<table><tr><td colspan='2'>[[2gcc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GCC FirstGlance]. <br> | <table><tr><td colspan='2'>[[2gcc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GCC FirstGlance]. <br> | ||
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATERF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATERF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gcc OCA], [http://pdbe.org/2gcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gcc RCSB], [http://www.ebi.ac.uk/pdbsum/2gcc PDBsum]</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=2gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gcc OCA], [http://pdbe.org/2gcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gcc RCSB], [http://www.ebi.ac.uk/pdbsum/2gcc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gcc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gc/2gcc_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gc/2gcc_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2gcc ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 09:59, 20 June 2018
SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED MEAN STRUCTURESOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED MEAN STRUCTURE
Structural highlights
Function[EF100_ARATH] Acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. Involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.[1] [2] [3] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.,Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M EMBO J. 1998 Sep 15;17(18):5484-96. PMID:9736626[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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