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1qle

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[[Image:1qle.gif|left|200px]]<br />
 
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<applet load="1qle" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qle, resolution 3.0&Aring;" />
 
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'''CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT'''<br />
 
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==Overview==
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==CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT==
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Cytochrome c oxidase catalyzes the reduction of oxygen to water. This, process is accompanied by the vectorial transport of protons across the, mitochondrial or bacterial membrane ("proton pumping"). The mechanism of, proton pumping is still a matter of debate. Many proposed mechanisms, require structural changes during the reaction cycle of cytochrome c, oxidase. Therefore, the structure of the cytochrome c oxidase was, determined in the completely oxidized and in the completely reduced states, at a temperature of 100 K. No ligand exchanges or other major structural, changes upon reduction of the cytochrome c oxidase from Paracoccus, denitrificans were observed. The three histidine Cu(B) ligands are well, defined in the oxidized and in the reduced states. These results are, hardly ... [[http://ispc.weizmann.ac.il/pmbin/getpm?10559205 (full description)]]
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<StructureSection load='1qle' size='340' side='right'caption='[[1qle]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qle]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. The May 2000 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 Oxidase'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_5 10.2210/rcsb_pdb/mom_2000_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QLE FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PC1:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PC1</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qle OCA], [https://pdbe.org/1qle PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qle RCSB], [https://www.ebi.ac.uk/pdbsum/1qle PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qle ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ql/1qle_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1qle ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). The mechanism of proton pumping is still a matter of debate. Many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. Therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a temperature of 100 K. No ligand exchanges or other major structural changes upon reduction of the cytochrome c oxidase from Paracoccus denitrificans were observed. The three histidine Cu(B) ligands are well defined in the oxidized and in the reduced states. These results are hardly compatible with the "histidine cycle" mechanisms formulated previously.
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==About this Structure==
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The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction.,Harrenga A, Michel H J Biol Chem. 1999 Nov 19;274(47):33296-9. PMID:10559205<ref>PMID:10559205</ref>
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1QLE is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]] and [[http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]] with CU, CA, MN, HEA, CUA and PC1 as [[http://en.wikipedia.org/wiki/ligands ligands]]. The following page contains interesting information on the relation of 1QLE with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb5_1.html Cytochrome c Oxidase]]. Active as [[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1]]. Structure known Active Sites: CA, CUA, CUB, HM3, HMA and MM. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QLE OCA]].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction., Harrenga A, Michel H, J Biol Chem. 1999 Nov 19;274(47):33296-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10559205 10559205]
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</div>
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<div class="pdbe-citations 1qle" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Cytochrome c Oxidase]]
[[Category: Cytochrome c Oxidase]]
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[[Category: Cytochrome-c oxidase]]
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
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[[Category: Protein complex]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Harrenga, A.]]
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[[Category: Harrenga A]]
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[[Category: Michel, H.]]
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[[Category: Michel H]]
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[[Category: CA]]
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[[Category: CU]]
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[[Category: CUA]]
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[[Category: HEA]]
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[[Category: MN]]
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[[Category: PC1]]
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[[Category: antibody complex]]
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[[Category: complex (oxidoreductase/antibody)]]
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[[Category: cytochrome oxidase]]
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[[Category: electron transport]]
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[[Category: transmembrane]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 16:01:21 2007''
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Current revision

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

PDB ID 1qle

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