3rko: Difference between revisions

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 <StructureSection load='3rko' size='340' side='right'caption='[[3rko]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 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 ''Complex I''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. The December 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 ''Complex I''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</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]] 3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H(+)-translocating) NADH:ubiquinone reductase (H(+)-translocating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [https://pdbe.org/3rko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [https://www.ebi.ac.uk/pdbsum/3rko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456] [[https://www.uniprot.org/uniprot/C6E9S6_ECOBD C6E9S6_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_00445] [[https://www.uniprot.org/uniprot/C6E9R4_ECOBD C6E9R4_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.[RuleBase:RU003639]  NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01394]
+[https://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 A resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.
-Structure of the membrane domain of respiratory complex I.,Efremov RG, Sazanov LA Nature. 2011 Aug 7. doi: 10.1038/nature10330. PMID:21822288<ref>PMID:21822288</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3rko" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[NADH-quinone oxidoreductase|NADH-quinone oxidoreductase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Complex I]]
-[[Category: Escherichia coli]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Efremov, R G]]
+[[Category: Efremov RG]]
-[[Category: Sazanov, L A]]
+[[Category: Sazanov LA]]
-[[Category: Complex i]]
-[[Category: Cytoplasmic membrane]]
-[[Category: Membrane protein]]
-[[Category: Nadh]]
-[[Category: Oxidoreductase]]
-[[Category: Proton pump]]
-[[Category: Ubiquinone]]