3cxh: Difference between revisions

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 ==Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.==
-<StructureSection load='3cxh' size='340' side='right' caption='[[3cxh]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3cxh' size='340' side='right'caption='[[3cxh]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3cxh]] is a 23 chain structure with sequence 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=3CXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CXH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3cxh]] is a 20 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=3CXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CXH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6PH:(1R)-2-(PHOSPHONOOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL+PENTADECANOATE'>6PH</scene>, <scene name='pdbligand=7PH:(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+TETRADECANOATE'>7PH</scene>, <scene name='pdbligand=8PE:(2R)-3-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-2-(TETRADECANOYLOXY)PROPYL+OCTADECANOATE'>8PE</scene>, <scene name='pdbligand=9PE:(1R)-2-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(HEPTANOYLOXY)METHYL]ETHYL+OCTADECANOATE'>9PE</scene>, <scene name='pdbligand=CN6:(2R,5R,11S,14R)-2-(BUTANOYLOXY)-5,8,11-TRIHYDROXY-5,11-DIOXIDO-16-OXO-14-[(PROPANOYLOXY)METHYL]-4,6,10,12,15-PENTAOXA-5,11-DIPHOSPHANONADEC-1-YL+UNDECANOATE'>CN6</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PH:(1R)-2-(PHOSPHONOOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL+PENTADECANOATE'>6PH</scene>, <scene name='pdbligand=7PH:(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+TETRADECANOATE'>7PH</scene>, <scene name='pdbligand=8PE:(2R)-3-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-2-(TETRADECANOYLOXY)PROPYL+OCTADECANOATE'>8PE</scene>, <scene name='pdbligand=9PE:(1R)-2-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(HEPTANOYLOXY)METHYL]ETHYL+OCTADECANOATE'>9PE</scene>, <scene name='pdbligand=CN6:(2R,5R,11S,14R)-2-(BUTANOYLOXY)-5,8,11-TRIHYDROXY-5,11-DIOXIDO-16-OXO-14-[(PROPANOYLOXY)METHYL]-4,6,10,12,15-PENTAOXA-5,11-DIPHOSPHANONADEC-1-YL+UNDECANOATE'>CN6</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cx5|3cx5]], [[1kyo|1kyo]], [[1kb9|1kb9]], [[1ezv|1ezv]]</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=3cxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cxh OCA], [https://pdbe.org/3cxh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cxh RCSB], [https://www.ebi.ac.uk/pdbsum/3cxh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cxh ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquinol--cytochrome-c_reductase Ubiquinol--cytochrome-c reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.2.2 1.10.2.2] </span></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=3cxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cxh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cxh RCSB], [http://www.ebi.ac.uk/pdbsum/3cxh PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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. [[http://www.uniprot.org/uniprot/CYB_YEAST CYB_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. [[http://www.uniprot.org/uniprot/QCR7_YEAST QCR7_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. QCR7 is involved in redox-linked proton pumping. [[http://www.uniprot.org/uniprot/QCR9_YEAST QCR9_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. QCR9 is required for formation of a fully functional complex. [[http://www.uniprot.org/uniprot/QCR2_YEAST QCR2_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. QCR2 is required for the assembly of the complex. [[http://www.uniprot.org/uniprot/CYC7_YEAST CYC7_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain. [[http://www.uniprot.org/uniprot/QCR8_YEAST QCR8_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. QCR8, together with cytochrome b, binds to ubiquinone. [[http://www.uniprot.org/uniprot/QCR1_YEAST QCR1_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. COR1 may mediate formation of the complex between cytochromes c and c1. [[http://www.uniprot.org/uniprot/CY1_YEAST CY1_YEAST]] Heme-containing 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. [[http://www.uniprot.org/uniprot/UCRI_YEAST UCRI_YEAST]] Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis. The complex couples electron transfer from ubiquinol to cytochrome c.
+[https://www.uniprot.org/uniprot/QCR1_YEAST QCR1_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. COR1 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/cx/3cxh_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cx/3cxh_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=3cxh ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3cxh" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Cytochrome bc1 complex|Cytochrome bc1 complex]]
+*[[Cytochrome bc1 3D structures|Cytochrome bc1 3D structures]]
-*[[Cytochrome c|Cytochrome c]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Ubiquinol--cytochrome-c reductase]]
+[[Category: Hunte C]]
-[[Category: Hunte, C]]
+[[Category: Solmaz SRN]]
-[[Category: Solmaz, S R.N]]
-[[Category: Complex iii]]
-[[Category: Cytochrome bc1 complex]]
-[[Category: Cytochrome c isoform-2]]
-[[Category: Electron transfer complex]]
-[[Category: Electron transport]]
-[[Category: Heme]]
-[[Category: Inner membrane]]
-[[Category: Iron]]
-[[Category: Iron-sulfur]]
-[[Category: Metal-binding]]
-[[Category: Mitochondrialtransmembrane complex]]
-[[Category: Mitochondrion]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphoprotein]]
-[[Category: Respiratory chain]]
-[[Category: Transient protein-protein interaction]]
-[[Category: Transit peptide]]
-[[Category: Transport]]