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- PDB-9rzv: E. coli cytochrome bd-I dimer bound to menaquinone -

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Basic information

Entry
Database: PDB / ID: 9rzv
TitleE. coli cytochrome bd-I dimer bound to menaquinone
Components
  • (Cytochrome bd-I ubiquinol oxidase subunit ...) x 3
  • Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
KeywordsOXIDOREDUCTASE / Oxireductase / Complex / Quinone / Substrate / membrane protein / Escherichia coli
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-9 / OXYGEN MOLECULE / Chem-PGT / Chem-POV / Ubiquinone-8 / Uncharacterized protein YnhF / Cytochrome bd-I ubiquinol oxidase subunit 1 ...: / PROTOPORPHYRIN IX CONTAINING FE / Chem-LPP / MENAQUINONE-9 / OXYGEN MOLECULE / Chem-PGT / Chem-POV / 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: 2.23 Å
Authorsvan der Velden, T.T. / Kayastha, K. / Bruenle, S. / Jeuken, L.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: To Be Published
Title: Molecular basis of quinone turnover and inhibition of a bd-type oxidase
Authors: van der Velden, T.T. / Kayastha, K. / Bruenle, S. / Jeuken, L.J.C.
History
DepositionJul 16, 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
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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)233,88636
Polymers215,5508
Non-polymers18,33628
Water1,38777
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 , 9 types, 105 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-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H80O2 / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: 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.: 2 / Source method: obtained synthetically / Formula: C49H74O4
#10: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#11: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C40H79O10P / Comment: phospholipid*YM
#12: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2PHENIX1.21.1_5286:model refinement
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530094 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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