9qef: Difference between revisions

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'''Unreleased structure'''


The entry 9qef is ON HOLD  until Paper Publication
==Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone==
<StructureSection load='9qef' size='340' side='right'caption='[[9qef]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9qef]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QEF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=7PH:(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+TETRADECANOATE'>7PH</scene>, <scene name='pdbligand=9XX:(2S)-1-(hexadecanoyloxy)propan-2-yl+(10S)-10-methyloctadecanoate'>9XX</scene>, <scene name='pdbligand=9YF:(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl+(9S)-9-methyloctadecanoate'>9YF</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DCQ:2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE'>DCQ</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IZL:[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl]+(10~{R})-10-methyldodecanoate'>IZL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=TRD:TRIDECANE'>TRD</scene>, <scene name='pdbligand=WUO:[(2~{R})-2-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propyl]+(10~{R})-10-methyloctadecanoate'>WUO</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=9qef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qef OCA], [https://pdbe.org/9qef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qef RCSB], [https://www.ebi.ac.uk/pdbsum/9qef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qef ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0R050_MYCS2 A0R050_MYCS2]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aerobic organisms obtain energy by linking electron transfer from NADH to O(2), through the respiratory chain, to transmembrane proton translocation. In mycobacteria the respiratory chain is branched; the membrane-bound electron carrier menaquinol (MQH(2)) donates electrons either to the O(2)-reducing cytochrome bd or a supercomplex that is composed of a complex (C) III(2) dimer flanked by two CIVs. Here, we measured the dimethyl-naphthoquinone (DMNQH(2,) a menaquinol analogue) oxidation:O(2) reduction activities of the CIII(2)CIV(2) supercomplex and cytochrome bd in the presence of an analogue (decylubiquinone, DCQ) of the mammalian electron carrier, ubiquinol. The data show that DCQH(2) inhibits both the CIII(2)CIV(2) and cytochrome bd activities, suggesting that DCQ/DCQH(2) interferes with both branches of the respiratory chain. Cryo-EM data of the M. smegmatis supercomplex shows that oxidized DCQ binds in the electron donor site (Q(o)) of CIII(2). Accordingly, growth of M. smegmatis cells was impaired in the presence of DCQ. Remarkably, DCQ also impairs intracellular growth of virulent M. tuberculosis cells in human primary macrophages suggesting that the compound could potentially be used as an adjuvant during tuberculosis disease treatment.


Authors: Kovalova, T., Krol, S., Brzezinski, P., Hogbom, M.
Mycobacterial respiratory chain enzymes and growth are inhibited by decylubiquinone.,Krol S, Kovalova T, Janczak M, Kalsum S, Akber M, Hogbom M, Brighenti S, Adelroth P, Brzezinski P Commun Biol. 2025 Dec 10;9(1):43. doi: 10.1038/s42003-025-09309-9. PMID:41372535<ref>PMID:41372535</ref>


Description: Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Krol, S]]
<div class="pdbe-citations 9qef" style="background-color:#fffaf0;"></div>
[[Category: Kovalova, T]]
== References ==
[[Category: Brzezinski, P]]
<references/>
[[Category: Hogbom, M]]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycolicibacterium smegmatis]]
[[Category: Brzezinski P]]
[[Category: Hogbom M]]
[[Category: Kovalova T]]
[[Category: Krol S]]

Latest revision as of 13:22, 10 February 2026

Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone

9qef, resolution 2.50Å

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