9QEF | pdb_00009qef

Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

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.

(2025) Commun Biol 9: 43-43

  • DOI: https://doi.org/10.1038/s42003-025-09309-9
  • Primary Citation of Related Structures:  
    9QEF

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitA [auth O],
M [auth C]
278Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4261
EC: 7.1.1.8
UniProt
Find proteins for A0R050 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R050
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitB [auth M],
N [auth G]
408Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4261
EC: 7.1.1.8
UniProt
Find proteins for A0R051 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R051
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitC [auth N],
O [auth H]
556Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4263
EC: 7.1.1.8
UniProt
Find proteins for A0R052 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R052
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinD [auth P],
P [auth I]
100Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_2575
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Probable cytochrome c oxidase subunit 3E [auth S],
Q [auth J]
203Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4260
EC: 7.1.1.9
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 4F [auth T],
R [auth K]
139Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4267
EC: 7.1.1.9
UniProt
Find proteins for A0R056 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R056
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1G [auth R],
S [auth L]
575Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: D806_022970
EC: 7.1.1.9
UniProt
Find proteins for A0A2U9PNL2 (Mycolicibacterium smegmatis (strain MKD8))
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UniProt GroupA0A2U9PNL2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome-c oxidaseH [auth Q],
T [auth X]
341Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4268
EC: 7.1.1.9
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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunitI [auth U],
U [auth Z]
79Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4693
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575J [auth V],
V [auth a]
157Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4692MSMEI_4575
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LpqE proteinK [auth W],
W [auth b]
186Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_6078
UniProt
Find proteins for A0R562 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]L [auth Y],
X [auth c]
236Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: sodCMSMEG_0835
EC: 1.15.1.1
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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified transmembrane proteinAA [auth A],
Y [auth E]
123Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: BIN_B_02039
UniProt
Find proteins for A0A653FDI6 (Mycolicibacterium smegmatis)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified peptideBA [auth B],
Z [auth F]
65Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEI_5553
UniProt
Find proteins for I7FT03 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IZL
Query on IZL

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HA [auth M],
XB [auth G]
[(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
C74 H133 O39 P
RFJQNGLGKTXNKA-YXJCWACHSA-N
CDL
Query on CDL

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AB [auth T]
BC [auth G]
CB [auth R]
EC [auth H]
FC [auth H]
AB [auth T],
BC [auth G],
CB [auth R],
EC [auth H],
FC [auth H],
GB [auth R],
GC [auth H],
KC [auth I],
LA [auth N],
LC [auth I],
MA [auth N],
NA [auth N],
PC [auth K],
RC [auth L],
TA [auth P],
VA [auth P],
ZC [auth L]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
WUO
Query on WUO

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FA [auth O],
MC [auth I],
UA [auth P],
UB [auth C]
acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
C72 H135 O24 P
NUQCUWACYIKWMU-RXWIBPKHSA-N
9YF
Query on 9YF

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ED [auth b],
IA [auth M],
OB [auth W],
YB [auth G]
(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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DB [auth R],
EB [auth R],
SC [auth L],
TC [auth L]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9
Query on MQ9

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EA [auth O]
HC [auth H]
OA [auth N]
QA [auth N]
TB [auth C]
EA [auth O],
HC [auth H],
OA [auth N],
QA [auth N],
TB [auth C],
VB [auth C],
ZA [auth T]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
3PE
Query on 3PE

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OC [auth J],
YA [auth S]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC
Query on HEC

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CA [auth O],
DA [auth O],
RB [auth C],
SB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DC [auth H],
IC [auth H],
KA [auth N],
PA [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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FD [auth b],
HD [auth c],
PB [auth W],
SA [auth N]
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
C38 H74 O4
LWLNRPPCJIGPLI-ZPGRZCPFSA-N
7PH
Query on 7PH

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AC [auth G],
CC [auth H],
JA [auth M],
WA [auth S],
ZB [auth G]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
DCQ (Subject of Investigation/LOI)
Query on DCQ

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JC [auth H]2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N
PLM
Query on PLM

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AD [auth L],
GD [auth c],
QB [auth W],
RA [auth N]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRD
Query on TRD

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BB [auth T]
DD [auth X]
JB [auth R]
KB [auth R]
NB [auth Q]
BB [auth T],
DD [auth X],
JB [auth R],
KB [auth R],
NB [auth Q],
NC [auth J],
QC [auth K],
XA [auth S],
XC [auth L],
YC [auth L]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
FES
Query on FES

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GA [auth M],
WB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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BD [auth X]
CD [auth X]
FB [auth R]
LB [auth Q]
MB [auth Q]
BD [auth X],
CD [auth X],
FB [auth R],
LB [auth Q],
MB [auth Q],
UC [auth L]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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IB [auth R],
WC [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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HB [auth R],
VC [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2019.0043

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release