9DM1 | pdb_00009dm1

Mycobacterial supercomplex malate:quinone oxidoreductase assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and aerobic respiration in mycobacteria.

Di Trani, J.M.Yu, J.Courbon, G.M.Lobez Rodriguez, A.P.Cheung, C.Y.Liang, Y.Coupland, C.E.Bueler, S.A.Cook, G.M.Brzezinski, P.Rubinstein, J.L.

(2025) Proc Natl Acad Sci U S A 122: e2423761122-e2423761122

  • DOI: https://doi.org/10.1073/pnas.2423761122
  • Primary Citation of Related Structures:  
    9DM1

  • PubMed Abstract: 

    To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from Mycobacterium smegmatis , 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.


  • Organizational Affiliation

    Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A [auth R],
D [auth L]
566Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for I7FHC3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitB [auth E],
C [auth F]
535Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for I7FGS8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupI7FGS8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]E [auth D],
F [auth G]
216Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.15.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0QQQ1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QQQ1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome aa3 subunit 2G [auth Q],
N [auth K]
312Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for A0R057 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R057
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome aa3 subunit 3H [auth S],
O [auth X]
203Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4I [auth T],
P [auth Z]
139Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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UniProt GroupA0R056
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit CtaJJ [auth U],
Q [auth a]
79Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575K [auth V],
R [auth b]
145Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved transmembrane proteinL [auth P],
S [auth J]
100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitM [auth O],
U [auth I]
223Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LpqE proteinT [auth c],
W
159Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunitV [auth Y],
X [auth M]
382Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7GD61 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Probable malate:quinone oxidoreductaseY [auth A]510Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.1.5.4
UniProt
Find proteins for A0QVL2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CA [auth R]
CB [auth S]
EB [auth T]
FB [auth T]
GB [auth T]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
9YF
Query on 9YF

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DC [auth I]
FC [auth Y]
GC [auth Y]
JC [auth W]
KC [auth M]
(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
C44 H85 O13 P
GRDWPDVMAXODDM-LZYRCPELSA-N
HEA
Query on HEA

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AA [auth R],
BA [auth R],
TA [auth L],
UA [auth L]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9
Query on MQ9

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CC [auth I]
FA [auth E]
GA [auth E]
JA [auth F]
PA [auth F]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
9Y0
Query on 9Y0

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DB [auth S]
IB [auth P]
OA [auth F]
QB [auth X]
VB [auth J]
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
C39 H76 N O8 P
DVXMEPWDARXHCX-OTMQOFQLSA-N
HEC
Query on HEC

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AC [auth I],
BC [auth I],
JB [auth O],
KB [auth O]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DA [auth E],
EA [auth E],
KA [auth F],
LA [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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IC [auth W],
XA [auth D],
YB [auth c],
ZA [auth G]
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
C38 H74 O4
LWLNRPPCJIGPLI-ZPGRZCPFSA-N
PLM
Query on PLM

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HC [auth W],
WA [auth D],
XB [auth c],
YA [auth G]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FES
Query on FES

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EC [auth Y],
MC [auth M]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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AB [auth Q]
BB [auth Q]
MB [auth K]
NB [auth K]
SA [auth L]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaJT162186

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references