1d3u: Difference between revisions

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-{{Seed}}
-[[Image:1d3u.png|left|200px]]
-<!--
+==TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI==
-The line below this paragraph, containing "STRUCTURE_1d3u", creates the "Structure Box" on the page.
+<StructureSection load='1d3u' size='340' side='right'caption='[[1d3u]], [[Resolution|resolution]] 2.40&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'>[[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>
-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]] 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>
-{{STRUCTURE_1d3u|  PDB=1d3u  |  SCENE=  }}
+</table>
+== Function ==
+[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>
+    <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/main_output.php?pdb_ID=1d3u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Recently the definition of the metazoan RNA polymerase II and archaeal core promoters has been expanded to include a region immediately upstream of the TATA box called the B recognition element (BRE), so named because eukaryal transcription factor TFIIB and its archaeal orthologue TFB interact with the element in a sequence-specific manner. Here we present the 2.4-A crystal structure of archaeal TBP and the C-terminal core of TFB (TFB(c)) in a complex with an extended TATA-box-containing promoter that provides a detailed picture of the stereospecific interactions between the BRE and a helix-turn-helix motif in the C-terminal cyclin repeat of TFB(c). This interaction is important in determining the level of basal transcription and explicitly defines the direction of transcription.
-===TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI===
+The structural basis for the oriented assembly of a TBP/TFB/promoter complex.,Littlefield O, Korkhin Y, Sigler PB Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13668-73. PMID:10570130<ref>PMID:10570130</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1d3u" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10570130}}, adds the Publication Abstract to the page
+*[[TATA-binding protein 3D structures|TATA-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10570130 is the PubMed ID number.
+*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_10570130}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-D3U is a 4 chains structure of sequences from [http://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].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:10570130</ref><references group="xtra"/>
 [[Category: Pyrococcus woesei]]
-[[Category: Korkhin, Y.]]
+[[Category: Korkhin Y]]
-[[Category: Littlefield, O.]]
+[[Category: Littlefield O]]
-[[Category: Sigler, P B.]]
+[[Category: Sigler PB]]
-[[Category: Hyperthermophile]]
-[[Category: Protein-dna complex]]
-[[Category: Transcription]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:40:58 2009''