1rio: Difference between revisions

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-{{Seed}}
-[[Image:1rio.png|left|200px]]
-<!--
+==Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA==
-The line below this paragraph, containing "STRUCTURE_1rio", creates the "Structure Box" on the page.
+<StructureSection load='1rio' size='340' side='right'caption='[[1rio]], [[Resolution|resolution]] 2.30&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'>[[1rio]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda] and [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RIO 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1rio|  PDB=1rio  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rio OCA], [https://pdbe.org/1rio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rio RCSB], [https://www.ebi.ac.uk/pdbsum/1rio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rio ProSAT]</span></td></tr>
+</table>
+== 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/ri/1rio_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=1rio ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cI protein of bacteriophage lambda (lambdacI) activates transcription by binding a DNA operator just upstream of the promoter and interacting with the RNA polymerase sigma subunit domain 4 (sigma(4)). We determined the crystal structure of the lambdacI/sigma(4)/DNA ternary complex at 2.3 A resolution. There are no conformational changes in either protein, which interact through an extremely small interface involving at most 6 amino acid residues. The interactions of the two proteins stabilize the binding of each protein to the DNA. The results provide insight into how activators can operate through a simple cooperative binding mechanism but affect different steps of the transcription initiation process.
-===Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA===
+Structure of a ternary transcription activation complex.,Jain D, Nickels BE, Sun L, Hochschild A, Darst SA Mol Cell. 2004 Jan 16;13(1):45-53. PMID:14731393<ref>PMID:14731393</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rio" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14731393}}, adds the Publication Abstract to the page
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14731393 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14731393}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus Lambda]]
-RIO is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIO OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:14731393</ref><references group="xtra"/>
-[[Category: Enterobacteria phage lambda]]
 [[Category: Thermus aquaticus]]
-[[Category: Darst, S A.]]
+[[Category: Darst SA]]
-[[Category: Hochschild, A.]]
+[[Category: Hochschild A]]
-[[Category: Jain, D.]]
+[[Category: Jain D]]
-[[Category: Nickels, B E.]]
+[[Category: Nickels BE]]
-[[Category: Sun, L.]]
+[[Category: Sun L]]
-[[Category: Helix-turn-helix]]
-[[Category: Transcription activation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:41:17 2009''