8E9G

Mycobacterial respiratory complex I with both quinone positions modelled


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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

Structure of mycobacterial respiratory complex I.

Liang, Y.Plourde, A.Bueler, S.A.Liu, J.Brzezinski, P.Vahidi, S.Rubinstein, J.L.

(2023) Proc Natl Acad Sci U S A 120: e2214949120-e2214949120

  • DOI: https://doi.org/10.1073/pnas.2214949120
  • Primary Citation of Related Structures:  
    8E9G, 8E9H, 8E9I

  • PubMed Abstract: 

    Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-component system response regulatorA [auth O]132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit B184Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AC [auth A]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CD [auth C]238Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit DE [auth D]442Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit EF [auth E]245Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.6.99.5
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit G794Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FH [auth F]443Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit I180Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HJ [auth H]408Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JK [auth J]252Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KL [auth K]99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase, L subunitM [auth L]629Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.6.99.5
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit N521Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase, M subunitO [auth M]529Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.6.99.5
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XP2 (Subject of Investigation/LOI)
Query on XP2

Download Ideal Coordinates CCD File 
DA [auth L](2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate
C51 H93 O24 P
QGXVEMBXLAEQBM-PUGXMYIYSA-N
MQ9 (Subject of Investigation/LOI)
Query on MQ9

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CA [auth H],
Q [auth B]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
GTP (Subject of Investigation/LOI)
Query on GTP

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T [auth G]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
Z [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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AA [auth I]
BA [auth I]
P [auth B]
U [auth G]
V [auth G]
AA [auth I],
BA [auth I],
P [auth B],
U [auth G],
V [auth G],
W [auth G],
Y [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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R [auth E],
S [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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X [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT162186
Canadian Institutes of Health Research (CIHR)CanadaPJT451412
Canadian Institutes of Health Research (CIHR)CanadaPJT173353
Canada Research ChairsCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection