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- PDB-9gy6: Mycobacterial cytochrome bc1:aa3 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 9gy6
TitleMycobacterial cytochrome bc1:aa3 with inhibitor
Components
  • (Cytochrome bc1 complex cytochrome ...) x 2
  • (Cytochrome c oxidase subunit ...) x 3
  • Cytochrome bc1 complex Rieske iron-sulfur subunit
  • Cytochrome c oxidase polypeptide 4
  • DUF5130 domain-containing protein
  • Secreted protein
  • Superoxide dismutase [Cu-Zn]
  • Transmembrane protein
KeywordsOXIDOREDUCTASE / membrane protein / inhibitor complex / mycobacterium / cytochrome bc
Function / homology
Function and homology information


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 ...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 / 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
Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / 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 ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-9Y0 / Chem-9YF / : / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 ...Chem-9Y0 / Chem-9YF / : / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 / MENAQUINONE-9 / PALMITIC ACID / Cytochrome c oxidase subunit 1 / Superoxide dismutase [Cu-Zn] / Transmembrane protein / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
Authorslamers, M.H. / Verma, A.K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative853903 Switzerland
Citation
Journal: NPJ Drug Discov / Year: 2025
Title: Structural and mechanistic study of a novel inhibitor analogue of cytochrome bc:aa.
Authors: Amit K Verma / Robbert Q Kim / Dirk A Lamprecht / Clara Aguilar-Pérez / Sarah Wong / Nicolas Veziris / Alexandra Aubry / José M Bartolomé-Nebreda / Rodrigo J Carbajo / Jennefer Wetzel / ...Authors: Amit K Verma / Robbert Q Kim / Dirk A Lamprecht / Clara Aguilar-Pérez / Sarah Wong / Nicolas Veziris / Alexandra Aubry / José M Bartolomé-Nebreda / Rodrigo J Carbajo / Jennefer Wetzel / Meindert H Lamers /
Abstract: Drug-resistant tuberculosis (TB) continues to challenge treatment options, necessitating the exploration of new compounds of novel targets. The mycobacterial respiratory complex cytochrome bc:aa has ...Drug-resistant tuberculosis (TB) continues to challenge treatment options, necessitating the exploration of new compounds of novel targets. The mycobacterial respiratory complex cytochrome bc:aa has emerged as a promising target, exemplified by the success of first-in-class inhibitor Q203 in phase 2 clinical trials. However, to fully exploit the potential of this target and to identify the best-in-class inhibitor more compounds need evaluation. Here, we introduce JNJ-2901, a novel Q203 analogue, that demonstrates activity against multidrug-resistant clinical strains at sub-nanomolar concentration and 4-log reduction in bacterial burden in a mouse model of TB infection. Inhibitory studies on purified enzymes validate the nanomolar inhibitions observed in mycobacterial cells. Additionally, cryo-EM structure analysis of cytochrome bc:aa bound to JNJ-2901 reveals the binding pocket at the menaquinol oxidation site (Qp), akin to other substate analogue inhibitors like Q203 and TB47. Validation of the binding site is further achieved by generating and isolating the JNJ-2901 resistant mutations in , followed by purification and resistance analysis of the resistant cytochrome bc:aa complex. Our comprehensive work lays the foundation for further clinical validations of JNJ-2901.
#1: Journal: Res Sq / Year: 2024
Title: Structural and mechanistic study of a novel inhibitor of M. tuberculosis cytochrome bc1:aa3
Authors: Lamers, M. / Verma, A. / Kim, R. / Lamprecht, D. / Perez, C.A. / Wong, S. / Veziris, N. / Aubry, A. / Bartolome-Nebreda, J.M. / Carbajo, R. / Wetzel, J.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome bc1 complex Rieske iron-sulfur subunit
B: Cytochrome bc1 complex cytochrome b subunit
C: Cytochrome bc1 complex cytochrome c subunit
D: Transmembrane protein
E: Cytochrome c oxidase subunit 2
F: Cytochrome c oxidase subunit 1
G: Cytochrome c oxidase subunit 3
H: Cytochrome c oxidase polypeptide 4
I: Secreted protein
J: DUF5130 domain-containing protein
L: Superoxide dismutase [Cu-Zn]
M: Cytochrome bc1 complex Rieske iron-sulfur subunit
N: Cytochrome bc1 complex cytochrome b subunit
O: Cytochrome bc1 complex cytochrome c subunit
P: Transmembrane protein
Q: Cytochrome c oxidase subunit 2
R: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase subunit 3
T: Cytochrome c oxidase polypeptide 4
U: Secreted protein
V: DUF5130 domain-containing protein
X: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)707,79181
Polymers662,35022
Non-polymers45,44159
Water3,801211
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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Protein , 6 types, 12 molecules AMDPHTIUJVLX

#1: Protein Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 reductase complex subunit QcrA / Rieske iron-sulfur protein / QcrA


Mass: 46383.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4262
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R051
#4: Protein Transmembrane protein / PRSAF1


Mass: 9531.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_2575
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QVH4
#8: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV / CtaF


Mass: 15177.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4267
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R056, cytochrome-c oxidase
#9: Protein Secreted protein / CtaJ


Mass: 8365.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4693
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R1B6
#10: Protein DUF5130 domain-containing protein / CtaI


Mass: 15910.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4692, MSMEI_4575
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R1B5
#11: Protein Superoxide dismutase [Cu-Zn] / SOD


Mass: 23232.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: sodC, MSMEG_0835
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQQ1, superoxide dismutase

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

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


Mass: 60262.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutations: F156Y, I182M, M189L, D309E, I312A
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4263
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R052, quinol-cytochrome-c reductase
#3: Protein Cytochrome bc1 complex cytochrome c subunit / QcrC


Mass: 27874.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4261
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R050, quinol-cytochrome-c reductase

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Cytochrome c oxidase subunit ... , 3 types, 6 molecules EQFRGS

#5: Protein Cytochrome c oxidase subunit 2 / CtaC


Mass: 38077.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4268
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R057, cytochrome-c oxidase
#6: Protein Cytochrome c oxidase subunit 1 / CtaD


Mass: 64162.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: D806_022970
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A2U9PNL2, cytochrome-c oxidase
#7: Protein Cytochrome c oxidase subunit 3 / CtaE


Mass: 22196.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4260
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R049, cytochrome-c oxidase

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Non-polymers , 14 types, 270 molecules

#12: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#13: 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.: 4 / Source method: obtained synthetically / Formula: C44H85O13P
#14: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#15: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 17 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#17: Chemical ChemComp-A1IRE / 6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide


Mass: 540.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24ClF3N4O3S
#18: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#19: Chemical ChemComp-MQ9 / MENAQUINONE-9


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


Mass: 717.996 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76NO8P
#21: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#22: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#23: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#24: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H64O2
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: cytochrome bc1:aa3 / Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT
Molecular weightValue: 0.667 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 3.3 mg/ml / Embedding 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: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00445054
ELECTRON MICROSCOPYf_angle_d0.79661168
ELECTRON MICROSCOPYf_dihedral_angle_d25.0277179
ELECTRON MICROSCOPYf_chiral_restr0.0456454
ELECTRON MICROSCOPYf_plane_restr0.0067512

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