6yj4
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==Structure of Yarrowia lipolytica complex I at 2.7 A== |
| - | <StructureSection load='6yj4' size='340' side='right'caption='[[6yj4]]' scene=''> | + | <StructureSection load='6yj4' size='340' side='right'caption='[[6yj4]], [[Resolution|resolution]] 2.70Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6yj4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YJ4 FirstGlance]. <br> |
| - | </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=6yj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yj4 OCA], [https://pdbe.org/6yj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yj4 RCSB], [https://www.ebi.ac.uk/pdbsum/6yj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yj4 ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.7Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=EHZ:~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl]+(3~{S})-3-oxidanyltetradecanethioate'>EHZ</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PLC:DIUNDECYL+PHOSPHATIDYL+CHOLINE'>PLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6yj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yj4 OCA], [https://pdbe.org/6yj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yj4 RCSB], [https://www.ebi.ac.uk/pdbsum/6yj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yj4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q6C674_YARLI Q6C674_YARLI] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-A-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine. | ||
| + | |||
| + | Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.,Grba DN, Hirst J Nat Struct Mol Biol. 2020 Aug 3. pii: 10.1038/s41594-020-0473-x. doi:, 10.1038/s41594-020-0473-x. PMID:32747785<ref>PMID:32747785</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6yj4" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Yarrowia lipolytica]] |
| + | [[Category: Grba D]] | ||
| + | [[Category: Hirst J]] | ||
Current revision
Structure of Yarrowia lipolytica complex I at 2.7 A
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