1nh2: Difference between revisions

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 ==Crystal structure of a yeast TFIIA/TBP/DNA complex==
-<StructureSection load='1nh2' size='340' side='right' caption='[[1nh2]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1nh2' size='340' side='right'caption='[[1nh2]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nh2]] is a 6 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=1NH2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NH2 FirstGlance]. <br>
+<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>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SPT15 OR BTF1 OR YER148W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), TOA1 OR YOR194C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), TOA2 OR YKL058W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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>
-<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=1nh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nh2 OCA], [http://pdbe.org/1nh2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nh2 RCSB], [http://www.ebi.ac.uk/pdbsum/1nh2 PDBsum]</span></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=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 ==
-[[http://www.uniprot.org/uniprot/TOA1_YEAST TOA1_YEAST]] TFIIA is a component of the transcription machinery of RNA polymerase II and implicated in the regulation of basal transcription. Interacts with TBP (the TATA-binding protein). [[http://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>  [[http://www.uniprot.org/uniprot/T2AG_YEAST T2AG_YEAST]] TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.<ref>PMID:1918049</ref>
+[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>
+     <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/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=1nh2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 ==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: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Bleichenbacher, M]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Richmond, T J]]
+[[Category: Bleichenbacher M]]
-[[Category: Tan, S]]
+[[Category: Richmond TJ]]
-[[Category: Transcription-dna complex]]
+[[Category: Tan S]]
-[[Category: Transcription/dna]]