1d3u: Difference between revisions

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OCA

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 ==TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI==
-<StructureSection load='1d3u' size='340' side='right' caption='[[1d3u]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1d3u' size='340' side='right'caption='[[1d3u]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1d3u]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_furiosus_subsp._woesei"_kanoksilapatham_et_al._2004 "pyrococcus furiosus subsp. woesei" kanoksilapatham et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D3U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1d3u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_woesei Pyrococcus woesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3U FirstGlance]. <br>
-</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=1d3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3u OCA], [http://pdbe.org/1d3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d3u RCSB], [http://www.ebi.ac.uk/pdbsum/1d3u PDBsum]</span></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]] 2.4&#8491;</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=1d3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3u OCA], [https://pdbe.org/1d3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3u RCSB], [https://www.ebi.ac.uk/pdbsum/1d3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3u ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TF2B_PYRWO TF2B_PYRWO]] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). [[http://www.uniprot.org/uniprot/TBP_PYRWO TBP_PYRWO]] General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the TATA box promoter element which lies close to the position of transcription initiation.
+[https://www.uniprot.org/uniprot/TBP_PYRWO TBP_PYRWO] General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the TATA box promoter element which lies close to the position of transcription initiation.
 == 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/d3/1d3u_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/1d3u_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1d3u ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 30: @@
 ==See Also==
-*[[TATA-Binding Protein|TATA-Binding Protein]]
+*[[TATA-binding protein 3D structures|TATA-binding protein 3D structures]]
-*[[Transcription initiation factor|Transcription initiation factor]]
+*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus furiosus subsp. woesei kanoksilapatham et al. 2004]]
+[[Category: Large Structures]]
-[[Category: Korkhin, Y]]
+[[Category: Pyrococcus woesei]]
-[[Category: Littlefield, O]]
+[[Category: Korkhin Y]]
-[[Category: Sigler, P B]]
+[[Category: Littlefield O]]
-[[Category: Gene regulation-dna complex]]
+[[Category: Sigler PB]]
-[[Category: Hyperthermophile]]
-[[Category: Protein-dna complex]]
-[[Category: Transcription]]