1kyo: Difference between revisions

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-[[Image:1kyo.gif|left|200px]]
- {{Structure
+==YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C==
-|PDB= 1kyo |SIZE=350|CAPTION= <scene name='initialview01'>1kyo</scene>, resolution 2.97&Aring;
+<StructureSection load='1kyo' size='340' side='right'caption='[[1kyo]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene> and <scene name='pdbligand=SMA:STIGMATELLIN A'>SMA</scene>
+<table><tr><td colspan='2'>[[1kyo]] 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]. The December 2002 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Cytochrome c''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2002_12 10.2210/rcsb_pdb/mom_2002_12]. The May 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Cytochrome bc1''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_5 10.2210/rcsb_pdb/mom_2011_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KYO FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.97&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</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=1kyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kyo OCA], [https://pdbe.org/1kyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kyo RCSB], [https://www.ebi.ac.uk/pdbsum/1kyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kyo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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/ky/1kyo_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/main_output.php?pdb_ID=1kyo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-A resolution. Cytochrome c is bound to subunit cytochrome c1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 x 10(6) s(-1). Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc1 complex can be regulated in response to respiratory conditions.
-'''YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C'''
+Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.,Lange C, Hunte C Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2800-5. PMID:11880631<ref>PMID:11880631</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1kyo" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-A resolution. Cytochrome c is bound to subunit cytochrome c1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 x 10(6) s(-1). Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc1 complex can be regulated in response to respiratory conditions.
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
+*[[Cytochrome bc1 3D structures|Cytochrome bc1 3D structures]]
-==About this Structure==
+== References ==
-KYO 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]. The following page contains interesting information on the relation of 1KYO with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb36_1.html Cytochrome c]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KYO OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c., Lange C, Hunte C, Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2800-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11880631 11880631]
+[[Category: Cytochrome bc1]]
 [[Category: Cytochrome c]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: RCSB PDB Molecule of the Month]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Ubiquinol--cytochrome-c reductase]]
+[[Category: Hunte C]]
-[[Category: Hunte, C.]]
+[[Category: Lange C]]
-[[Category: Lange, C.]]
-[[Category: FES]]
-[[Category: HEM]]
-[[Category: SMA]]
-[[Category: antibody fv fragment mediated crystallization]]
-[[Category: electron transfer complex]]
-[[Category: enzyme substrate complex]]
-[[Category: multisubunit membrane protein complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:23:59 2008''