2km4: Difference between revisions

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 ==Solution structure of Rtt103 CTD interacting domain==
-<StructureSection load='2km4' size='340' side='right' caption='[[2km4]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2km4' size='340' side='right'caption='[[2km4]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2km4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KM4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2km4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KM4 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RTT103, YDR289C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2km4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2km4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2km4 RCSB], [http://www.ebi.ac.uk/pdbsum/2km4 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=2km4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2km4 OCA], [https://pdbe.org/2km4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2km4 RCSB], [https://www.ebi.ac.uk/pdbsum/2km4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2km4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RT103_YEAST RT103_YEAST]] Involved in transcription termination by RNA polymerase II and in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:15565157</ref>
+[https://www.uniprot.org/uniprot/RT103_YEAST RT103_YEAST] Involved in transcription termination by RNA polymerase II and in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:15565157</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/km/2km4_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/2km4_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=2km4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTD-interacting domains (CIDs) that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CIDs of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single-residue mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3' end processing site in vivo. We suggest that this cooperativity provides a signal-response mechanism to ensure that its action is confined only to proper polyadenylation sites where Ser2 phosphorylation density is highest.
-Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.,Lunde BM, Reichow SL, Kim M, Suh H, Leeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G Nat Struct Mol Biol. 2010 Oct;17(10):1195-201. Epub 2010 Sep 5. PMID:20818393<ref>PMID:20818393</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Becker, R]]
+[[Category: Becker R]]
-[[Category: Buratowski, S]]
+[[Category: Buratowski S]]
-[[Category: Kim, M]]
+[[Category: Kim M]]
-[[Category: Leeper, T C]]
+[[Category: Leeper TC]]
-[[Category: Lunde, B M]]
+[[Category: Lunde BM]]
-[[Category: Meinhart, A]]
+[[Category: Meinhart A]]
-[[Category: Reichow, S]]
+[[Category: Reichow S]]
-[[Category: Varani, G]]
+[[Category: Varani G]]
-[[Category: Ctd-interacting domain]]
-[[Category: Dna-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Rna polymerase ii binding protein]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]
-[[Category: Transcription termination]]