1nh2: Difference between revisions

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-{{Seed}}
-[[Image:1nh2.png|left|200px]]
-<!--
+==Crystal structure of a yeast TFIIA/TBP/DNA complex==
-The line below this paragraph, containing "STRUCTURE_1nh2", creates the "Structure Box" on the page.
+<StructureSection load='1nh2' size='340' side='right'caption='[[1nh2]], [[Resolution|resolution]] 1.90&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'>[[1nh2]] is a 6 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=1NH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NH2 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>
-{{STRUCTURE_1nh2|  PDB=1nh2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nh2 OCA], [https://pdbe.org/1nh2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nh2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nh2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nh2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TBP_YEAST TBP_YEAST] General transcription factor that functions at the core of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:9618449</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</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/nh/1nh2_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=1nh2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RNA polymerase II-dependent transcription requires the assembly of a multi-protein, preinitiation complex on core promoter elements. Transcription factor IID (TFIID) comprising the TATA box-binding protein (TBP) and TBP-associated factors (TAFs) is responsible for promoter recognition in this complex. Subsequent association of TFIIA and TFIIB provides enhanced complex stability. TFIIA is required for transcriptional stimulation by certain viral and cellular activators, and favors formation of the preinitiation complex in the presence of repressor NC2. The X-ray structures of human and yeast TBP/TFIIA/DNA complexes at 2.1A and 1.9A resolution, respectively, are presented here and seen to resemble each other closely. The interactions made by human TFIIA with TBP and DNA within and upstream of the TATA box, including those involving water molecules, are described and compared to the yeast structure. Of particular interest is a previously unobserved region of TFIIA that extends the binding interface with TBP in the yeast, but not in the human complex, and that further elucidates biochemical and genetic results.
-===Crystal structure of a yeast TFIIA/TBP/DNA complex===
+Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes.,Bleichenbacher M, Tan S, Richmond TJ J Mol Biol. 2003 Sep 26;332(4):783-93. PMID:12972251<ref>PMID:12972251</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1nh2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12972251}}, 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 12972251 is the PubMed ID number.
+*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12972251}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-NH2 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NH2 OCA].
+[[Category: Large Structures]]
-==Reference==
-Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes., Bleichenbacher M, Tan S, Richmond TJ, J Mol Biol. 2003 Sep 26;332(4):783-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12972251 12972251]
-[[Category: Protein complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Bleichenbacher, M.]]
+[[Category: Bleichenbacher M]]
-[[Category: Richmond, T J.]]
+[[Category: Richmond TJ]]
-[[Category: Tan, S.]]
+[[Category: Tan S]]
-[[Category: Transcription/dna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:51:38 2008''