1kb9: Difference between revisions

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-{{Seed}}
-[[Image:1kb9.png|left|200px]]
-<!--
+==YEAST CYTOCHROME BC1 COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1kb9", creates the "Structure Box" on the page.
+<StructureSection load='1kb9' size='340' side='right'caption='[[1kb9]], [[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'>[[1kb9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KB9 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=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PCF:1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE'>PCF</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</scene>, <scene name='pdbligand=PIE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL'>PIE</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UQ6:5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL'>UQ6</scene></td></tr>
-{{STRUCTURE_1kb9|  PDB=1kb9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kb9 OCA], [https://pdbe.org/1kb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kb9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kb9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/QCR6_YEAST QCR6_YEAST] Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is part of the mitochondrial respiratory chain that generates an electrochemical potential coupled to ATP synthesis. The complex couples electron transfer from ubiquinol to cytochrome c. QCR6 may mediate formation of the complex between cytochromes c and c1.
+== 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/kb/1kb9_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=1kb9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biochemical data have shown that specific, tightly bound phospholipids are essential for activity of the cytochrome bc1 complex (QCR), an integral membrane protein of the respiratory chain. However, the structure and function of such phospholipids are not yet known. Here we describe five phospholipid molecules and one detergent molecule in the X-ray structure of yeast QCR at 2.3 A resolution. Their individual binding sites suggest specific roles in facilitating structural and functional integrity of the enzyme. Interestingly, a phosphatidylinositol molecule is bound in an unusual interhelical position near the flexible linker region of the Rieske iron-sulfur protein. Two possible proton uptake pathways at the ubiquinone reduction site have been identified: the E/R and the CL/K pathway. Remarkably, cardiolipin is positioned at the entrance to the latter. We propose that cardiolipin ensures structural integrity of the proton-conducting protein environment and takes part directly in proton uptake. Site-directed mutagenesis of ligating residues confirmed the importance of the phosphatidylinositol- and cardiolipin-binding sites.
-===YEAST CYTOCHROME BC1 COMPLEX===
+Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure.,Lange C, Nett JH, Trumpower BL, Hunte C EMBO J. 2001 Dec 3;20(23):6591-600. PMID:11726495<ref>PMID:11726495</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1kb9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11726495}}, adds the Publication Abstract to the page
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11726495 is the PubMed ID number.
+*[[Cytochrome bc1 3D structures|Cytochrome bc1 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_11726495}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-KB9 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KB9 OCA].
+[[Category: Large Structures]]
-==Reference==
-Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure., Lange C, Nett JH, Trumpower BL, Hunte C, EMBO J. 2001 Dec 3;20(23):6591-600. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11726495 11726495]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Ubiquinol--cytochrome-c reductase]]
+[[Category: Hunte C]]
-[[Category: Hunte, C.]]
+[[Category: Lange C]]
-[[Category: Lange, C.]]
+[[Category: Nett JH]]
-[[Category: Nett, J H.]]
+[[Category: Trumpower BL]]
-[[Category: Trumpower, B L.]]
-[[Category: Cardiolipin]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphatidylcholin]]
-[[Category: Phosphatidylethanolamin]]
-[[Category: Phosphatidylinositol]]
-[[Category: Stigmatellin]]
-[[Category: Ubiquinone]]
-[[Category: Undecyl-maltopyranoside]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 10:04:33 2008''