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- PDB-9dm1: Mycobacterial supercomplex malate:quinone oxidoreductase assembly -

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Basic information

Entry
Database: PDB / ID: 9dm1
TitleMycobacterial supercomplex malate:quinone oxidoreductase assembly
Components
  • (Cytochrome aa3 subunit ...) x 2
  • (Cytochrome bc1 complex cytochrome ...) x 2
  • (Cytochrome c oxidase subunit ...) x 2
  • Conserved transmembrane protein
  • Cytochrome bc1 complex Rieske iron-sulfur subunit
  • Cytochrome c oxidase polypeptide 4
  • LpqE protein
  • Probable malate:quinone oxidoreductase
  • Superoxide dismutase [Cu-Zn]
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
KeywordsMEMBRANE PROTEIN / Electron transport chain / mycobacterial CIII2CIV2 supercomplex
Function / homology
Function and homology information


malate dehydrogenase (quinone) / L-malate dehydrogenase (quinone) activity / 2-hydroxyglutarate dehydrogenase activity / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase ...malate dehydrogenase (quinone) / L-malate dehydrogenase (quinone) activity / 2-hydroxyglutarate dehydrogenase activity / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport / tricarboxylic acid cycle / respiratory electron transport chain / monooxygenase activity / electron transport chain / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Malate:quinone-oxidoreductase / Malate:quinone oxidoreductase (Mqo) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB ...Malate:quinone-oxidoreductase / Malate:quinone oxidoreductase (Mqo) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome c / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 ...Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / PALMITIC ACID / Cytochrome c oxidase subunit 1 / Probable malate:quinone oxidoreductase / Probable cytochrome c oxidase subunit 3 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 complex cytochrome c subunit / Cytochrome c oxidase polypeptide 4 / Uncharacterized protein / Superoxide dismutase [Cu-Zn] / Cytochrome bc1 complex Rieske iron-sulfur subunit / cytochrome-c oxidase / LpqE protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDi Trani, J.M. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)JT162186 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and aerobic respiration in mycobacteria.
Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / ...Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / John L Rubinstein /
Abstract: To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged ...To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged the vesicles with electron cryomicroscopy. We show that this analysis allows determination of the structure of both mycobacterial ATP synthase and the supercomplex of respiratory complexes III and IV in their native membrane. The latter structure reveals that the enzyme malate:quinone oxidoreductase (Mqo) physically associates with the respiratory supercomplex, an interaction that is lost on extraction of the proteins from the lipid bilayer. Mqo catalyzes an essential reaction in the Krebs cycle, and in vivo survival of mycobacterial pathogens is compromised when its activity is absent. We show with high-speed spectroscopy that the Mqo:supercomplex interaction enables rapid electron transfer from malate to the supercomplex. Further, the respiratory supercomplex is necessary for malate-driven, but not NADH-driven, electron transport chain activity and oxygen consumption. Together, these findings indicate a connection between the Krebs cycle and aerobic respiration that directs electrons along a single branch of the mycobacterial electron transport chain.
History
DepositionSep 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Cytochrome c oxidase subunit 1
E: Cytochrome bc1 complex cytochrome b subunit
F: Cytochrome bc1 complex cytochrome b subunit
L: Cytochrome c oxidase subunit 1
D: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
Q: Cytochrome aa3 subunit 2
S: Cytochrome aa3 subunit 3
T: Cytochrome c oxidase polypeptide 4
U: Cytochrome c oxidase subunit CtaJ
V: Uncharacterized protein MSMEG_4692/MSMEI_4575
P: Conserved transmembrane protein
O: Cytochrome bc1 complex cytochrome c subunit
K: Cytochrome aa3 subunit 2
X: Cytochrome aa3 subunit 3
Z: Cytochrome c oxidase polypeptide 4
a: Cytochrome c oxidase subunit CtaJ
b: Uncharacterized protein MSMEG_4692/MSMEI_4575
J: Conserved transmembrane protein
c: LpqE protein
I: Cytochrome bc1 complex cytochrome c subunit
Y: Cytochrome bc1 complex Rieske iron-sulfur subunit
W: LpqE protein
M: Cytochrome bc1 complex Rieske iron-sulfur subunit
A: Probable malate:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)773,33391
Polymers720,00325
Non-polymers53,32966
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules RLUa

#1: Protein Cytochrome c oxidase subunit 1


Mass: 63296.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0A0K0XH24, cytochrome-c oxidase
#7: Protein Cytochrome c oxidase subunit CtaJ


Mass: 8365.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FQK8

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Cytochrome bc1 complex cytochrome ... , 2 types, 4 molecules EFOI

#2: Protein Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 reductase complex subunit QcrB


Mass: 59110.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FGS8, quinol-cytochrome-c reductase
#10: Protein Cytochrome bc1 complex cytochrome c subunit


Mass: 23183.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FPH1, quinol-cytochrome-c reductase

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Protein , 7 types, 13 molecules DGTZVbPJcWYMA

#3: Protein Superoxide dismutase [Cu-Zn]


Mass: 21221.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G2H6, superoxide dismutase
#6: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15177.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FPH7, cytochrome-c oxidase
#8: Protein Uncharacterized protein MSMEG_4692/MSMEI_4575


Mass: 14808.747 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R1B5
#9: Protein Conserved transmembrane protein


Mass: 11329.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155
#11: Protein LpqE protein


Mass: 16412.873 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7GFE1
#12: Protein Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 reductase complex subunit QcrA


Mass: 42210.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7GD61
#13: Protein Probable malate:quinone oxidoreductase / MQO / Malate dehydrogenase [quinone]


Mass: 54970.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVL2, malate dehydrogenase (quinone)

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Cytochrome aa3 subunit ... , 2 types, 4 molecules QKSX

#4: Protein Cytochrome aa3 subunit 2


Mass: 35201.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7GD63, cytochrome-c oxidase
#5: Protein Cytochrome aa3 subunit 3 / Probable cytochrome c oxidase subunit 3


Mass: 22196.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R049

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Non-polymers , 11 types, 66 molecules

#14: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#15: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#16: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#17: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#18: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C56H80O2
#19: Chemical
ChemComp-9Y0 / (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H76NO8P
#20: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#21: Chemical
ChemComp-9XX / (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate / (S)-1-(palmitoyloxy)propan-2-yl (S)-10-methyloctadecanoate


Mass: 594.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H74O4
#22: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#23: Chemical
ChemComp-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


Mass: 853.112 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85O13P
#24: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis
Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 41.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145585 / Symmetry type: POINT

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