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- PDB-9sfj: E.coli cytochrome bd-I dimer in the MK bound open and closed state -

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Basic information

Entry
Database: PDB / ID: 9sfj
TitleE.coli cytochrome bd-I dimer in the MK bound open and closed state
Components
  • (Cytochrome bd-I ubiquinol oxidase subunit ...) x 3
  • Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
KeywordsOXIDOREDUCTASE / Respiration / Complex / Cytochrome
Function / homology
Function and homology information


quinol oxidase (electrogenic, proton-motive force generating) / oxidoreductase activity, acting on diphenols and related substances as donors / cytochrome complex / aerobic electron transport chain / outer membrane / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cellular response to hypoxia / electron transfer activity / heme binding ...quinol oxidase (electrogenic, proton-motive force generating) / oxidoreductase activity, acting on diphenols and related substances as donors / cytochrome complex / aerobic electron transport chain / outer membrane / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cellular response to hypoxia / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Cyd operon protein YbgT / Membrane bound YbgT-like / Membrane bound YbgT-like protein / Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Chem-LPP / MENAQUINONE 8 / OXYGEN MOLECULE / Ubiquinone-8 / Uncharacterized protein YnhF / Cytochrome bd-I ubiquinol oxidase subunit 1 / Cytochrome bd-I ubiquinol oxidase subunit 2 / Cytochrome bd-I ubiquinol oxidase subunit X
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
Authorsvan der Velden, T.T. / Kaystha, K. / Bruenle, S. / Jeuken, L.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: Sci Adv / Year: 2026
Title: Visualizing the mechanism of quinol oxidation and inhibition of a -type oxidase using cryo-EM.
Authors: Tijn T van der Velden / Kanwal Kayastha / Famke Pelser / Steffen Brünle / Lars J C Jeuken /
Abstract: Cytochrome is a prokaryotic terminal oxidase recognized as an antibiotic target against various pathogens. Despite its critical role in respiration, failure to capture the mechanism of quinol ...Cytochrome is a prokaryotic terminal oxidase recognized as an antibiotic target against various pathogens. Despite its critical role in respiration, failure to capture the mechanism of quinol oxidation and inhibition prohibits structure guided drug discovery. Here, we present cryo-electron microscopy structures of cytochrome -I in monomeric and dimeric forms, in several quinone and inhibitor-bound states. We identify a dynamic Q-loop lid that undergoes a disorder-to-order transition upon substrate binding to the dimer, completing the active site and enabling catalysis. Structure-guided mutagenesis confirms Tyr243 and Arg298 as conserved catalytic residues only found in long Q-loop oxidases, highlighting evolutionary divergence from other subfamilies. Inhibition by Aurachin D triggers refolding of the active site, occluding substrate access via an Asp239-mediated mechanism. The structural and mechanistic insights presented here establish a comprehensive framework, opening paths for drug discovery against oxidases.
History
DepositionAug 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jun 10, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome bd-I ubiquinol oxidase subunit 1
B: Cytochrome bd-I ubiquinol oxidase subunit 2
H: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
X: Cytochrome bd-I ubiquinol oxidase subunit X
a: Cytochrome bd-I ubiquinol oxidase subunit 1
b: Cytochrome bd-I ubiquinol oxidase subunit 2
h: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
x: Cytochrome bd-I ubiquinol oxidase subunit X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,55727
Polymers215,5508
Non-polymers12,00719
Water1629
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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Cytochrome bd-I ubiquinol oxidase subunit ... , 3 types, 6 molecules AaBbXx

#1: Protein Cytochrome bd-I ubiquinol oxidase subunit 1 / Cytochrome bd-I oxidase subunit I / Cytochrome d ubiquinol oxidase subunit I


Mass: 58251.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cydA, cyd-1, b0733, JW0722 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABJ9, quinol oxidase (electrogenic, proton-motive force generating)
#2: Protein Cytochrome bd-I ubiquinol oxidase subunit 2 / Cytochrome bd-I oxidase subunit II / Cytochrome d ubiquinol oxidase subunit II


Mass: 42479.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cydB, cyd-2, b0734, JW0723 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABK2, quinol oxidase (electrogenic, proton-motive force generating)
#4: Protein/peptide Cytochrome bd-I ubiquinol oxidase subunit X / Cytochrome bd-I oxidase subunit X / Cytochrome d ubiquinol oxidase subunit X


Mass: 4043.663 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cydX, ybgT, b4515, JW0724 / Production host: Escherichia coli (E. coli)
References: UniProt: P56100, quinol oxidase (electrogenic, proton-motive force generating)

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Protein/peptide , 1 types, 2 molecules Hh

#3: Protein/peptide Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)


Mass: 2999.651 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ynhF, b4602, JW1649.1 / Production host: Escherichia coli (E. coli) / References: UniProt: A5A618

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Non-polymers , 7 types, 28 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-A1JN4 / TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE


Mass: 636.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O5
#7: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H72O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: E.coli cytochrome bd-I monomer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARC4.6.0CTF correction
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224083 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415886
ELECTRON MICROSCOPYf_angle_d1.97121610
ELECTRON MICROSCOPYf_dihedral_angle_d17.1752412
ELECTRON MICROSCOPYf_chiral_restr0.0372339
ELECTRON MICROSCOPYf_plane_restr0.0042595

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