2cf4: Difference between revisions

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-[[Image:2cf4.png|left|200px]]
-<!--
+==Pyrococcus horikoshii TET1 peptidase can assemble into a tetrahedron or a large octahedral shell==
-The line below this paragraph, containing "STRUCTURE_2cf4", creates the "Structure Box" on the page.
+<StructureSection load='2cf4' size='340' side='right'caption='[[2cf4]], [[Resolution|resolution]] 3.08&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'>[[2cf4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CF4 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]] 3.08&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2cf4|  PDB=2cf4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cf4 OCA], [https://pdbe.org/2cf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cf4 RCSB], [https://www.ebi.ac.uk/pdbsum/2cf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cf4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O58255_PYRHO O58255_PYRHO]
+== 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/cf/2cf4_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=2cf4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.
-===PYROCOCCUS HORIKOSHII TET1 PEPTIDASE CAN ASSEMBLE INTO A TETRAHEDRON OR A LARGE OCTAHEDRAL SHELL===
+An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.,Schoehn G, Vellieux FM, Asuncion Dura M, Receveur-Brechot V, Fabry CM, Ruigrok RW, Ebel C, Roussel A, Franzetti B J Biol Chem. 2006 Nov 24;281(47):36327-37. Epub 2006 Sep 14. PMID:16973604<ref>PMID:16973604</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16973604}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2cf4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16973604 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16973604}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2cf4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF4 OCA].
+[[Category: Pyrococcus horikoshii OT3]]
+[[Category: Dura MA]]
-==Reference==
+[[Category: Franzetti B]]
-<ref group="xtra">PMID:016973604</ref><ref group="xtra">PMID:011980710</ref><references group="xtra"/>
+[[Category: Roussel A]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Schoehn G]]
-[[Category: Dura, M A.]]
+[[Category: Vellieux FMD]]
-[[Category: Franzetti, B.]]
-[[Category: Roussel, A.]]
-[[Category: Schoehn, G.]]
-[[Category: Vellieux, F M.D.]]
-[[Category: Aminopeptidase]]
-[[Category: Archaea]]
-[[Category: Hydrolase]]
-[[Category: Hyperthermophile]]
-[[Category: Metalloprotein]]
-[[Category: Tetrahedral]]