2hik: Difference between revisions

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-[[Image:2hik.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2hik", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2hik|  PDB=2hik  |  SCENE=  }}
-'''heterotrimeric PCNA sliding clamp'''
+==heterotrimeric PCNA sliding clamp==
+<StructureSection load='2hik' size='340' side='right'caption='[[2hik]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hik]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HIK FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2hik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hik OCA], [https://pdbe.org/2hik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hik RCSB], [https://www.ebi.ac.uk/pdbsum/2hik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hik 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/hi/2hik_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=2hik ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA sliding clamps encircle DNA and provide binding sites for many DNA-processing enzymes. However, it is largely unknown how sliding clamps like proliferating cell nuclear antigen (PCNA) coordinate multistep DNA transactions. We have determined structures of Sulfolobus solfataricus DNA ligase and heterotrimeric PCNA separately by X-ray diffraction and in complex by small-angle X-ray scattering (SAXS). Three distinct PCNA subunits assemble into a protein ring resembling the homotrimeric PCNA of humans but with three unique protein-binding sites. In the absence of nicked DNA, the Sulfolobus solfataricus DNA ligase has an open, extended conformation. When complexed with heterotrimeric PCNA, the DNA ligase binds to the PCNA3 subunit and ligase retains an open, extended conformation. A closed, ring-shaped conformation of ligase catalyzes a DNA end-joining reaction that is strongly stimulated by PCNA. This open-to-closed switch in the conformation of DNA ligase is accommodated by a malleable interface with PCNA that serves as an efficient platform for DNA ligation.
-==Overview==
+A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.,Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T Mol Cell. 2006 Oct 20;24(2):279-91. PMID:17052461<ref>PMID:17052461</ref>
-DNA sliding clamps encircle DNA and provide binding sites for many DNA-processing enzymes. However, it is largely unknown how sliding clamps like proliferating cell nuclear antigen (PCNA) coordinate multistep DNA transactions. We have determined structures of Sulfolobus solfataricus DNA ligase and heterotrimeric PCNA separately by X-ray diffraction and in complex by small-angle X-ray scattering (SAXS). Three distinct PCNA subunits assemble into a protein ring resembling the homotrimeric PCNA of humans but with three unique protein-binding sites. In the absence of nicked DNA, the Sulfolobus solfataricus DNA ligase has an open, extended conformation. When complexed with heterotrimeric PCNA, the DNA ligase binds to the PCNA3 subunit and ligase retains an open, extended conformation. A closed, ring-shaped conformation of ligase catalyzes a DNA end-joining reaction that is strongly stimulated by PCNA. This open-to-closed switch in the conformation of DNA ligase is accommodated by a malleable interface with PCNA that serves as an efficient platform for DNA ligation.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-HIK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HIK OCA].
+</div>
+<div class="pdbe-citations 2hik" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA., Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T, Mol Cell. 2006 Oct 20;24(2):279-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17052461 17052461]
+*[[Proliferating cell nuclear antigen 3D structures|Proliferating cell nuclear antigen 3D structures]]
-[[Category: Protein complex]]
+== References ==
-[[Category: Sulfolobus solfataricus]]
+<references/>
-[[Category: Ellenberger, T.]]
+__TOC__
-[[Category: Pascal, J M.]]
+</StructureSection>
-[[Category: Tsodikov, O V.]]
+[[Category: Large Structures]]
-[[Category: Dna replication]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: Heterotrimer]]
+[[Category: Ellenberger T]]
-[[Category: Pcna sliding clamp]]
+[[Category: Pascal JM]]
-[[Category: Processivity factor]]
+[[Category: Tsodikov OV]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:20:15 2008''