8OVD

Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex.

Riepl, D.Gamiz-Hernandez, A.P.Kovalova, T.Krol, S.M.Mader, S.L.Sjostrand, D.Hogbom, M.Brzezinski, P.Kaila, V.R.I.

(2024) Nat Commun 15: 5276-5276

  • DOI: https://doi.org/10.1038/s41467-024-49628-9
  • Primary Citation of Related Structures:  
    8OVC, 8OVD

  • PubMed Abstract: 

    Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III 2 IV 2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, 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
Membrane Entity: Yes 
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
Membrane Entity: Yes 
UniProt
Find proteins for A0R051 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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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
Membrane Entity: Yes 
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
Membrane Entity: Yes 
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QVH4
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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
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R049
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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
Membrane Entity: Yes 
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
Membrane Entity: Yes 
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
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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunitI [auth U],
U [auth Z]
79Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEG_4693
Membrane Entity: Yes 
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B6
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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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UniProt GroupA0R1B5
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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
Membrane Entity: Yes 
UniProt
Find proteins for A0R562 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R562
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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
Membrane Entity: Yes 
UniProt
Find proteins for A0QQQ1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IZL
Query on IZL

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DA [auth M],
WB [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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BC [auth H]
CB [auth R]
CC [auth H]
DC [auth H]
IA [auth N]
BC [auth H],
CB [auth R],
CC [auth H],
DC [auth H],
IA [auth N],
IC [auth I],
JA [auth N],
JC [auth I],
KA [auth N],
LC [auth J],
QA [auth P],
QC [auth L],
TB [auth C],
WA [auth T],
YA [auth R]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
WUO
Query on WUO

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BA [auth O],
KC [auth I],
RA [auth P],
SB [auth C]
acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
C72 H135 O24 P
NUQCUWACYIKWMU-RXWIBPKHSA-N
9YF
Query on 9YF

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BD [auth b],
EA [auth M],
KB [auth W],
XB [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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AB [auth R],
RC [auth L],
SC [auth L],
ZA [auth R]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9
Query on MQ9

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AA [auth O]
EC [auth H]
FC [auth H]
GA [auth M]
HC [auth H]
AA [auth O],
EC [auth H],
FC [auth H],
GA [auth M],
HC [auth H],
LA [auth N],
MA [auth N],
OA [auth N],
OC [auth K],
RB [auth C],
UB [auth G],
VA [auth T]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
3PE
Query on 3PE

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

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PB [auth C],
QB [auth C],
Y [auth O],
Z [auth O]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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AC [auth H],
GC [auth H],
HA [auth N],
NA [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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

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FA [auth M],
PA [auth N],
SA [auth S],
YB [auth G],
ZB [auth H]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
PLM
Query on PLM

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CD [auth b],
ED [auth c],
MB [auth W],
NB [auth Y]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRD
Query on TRD

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AD [auth X]
FB [auth R]
GB [auth R]
JB [auth Q]
MC [auth J]
AD [auth X],
FB [auth R],
GB [auth R],
JB [auth Q],
MC [auth J],
PC [auth K],
TA [auth S],
WC [auth L],
XA [auth T],
XC [auth L]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
FES
Query on FES

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

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BB [auth R]
HB [auth Q]
IB [auth Q]
TC [auth L]
YC [auth X]
BB [auth R],
HB [auth Q],
IB [auth Q],
TC [auth L],
YC [auth X],
ZC [auth X]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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EB [auth R],
VC [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2024-07-17
    Type: Initial release