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- EMDB-54414: E. coli cytochrome bd-I dimer bound to menaquinone -

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Basic information

Entry
Database: EMDB / ID: EMD-54414
TitleE. coli cytochrome bd-I dimer bound to menaquinone
Map data
Sample
  • Complex: E. coli cytochrome bd-I
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
KeywordsOxireductase / Complex / Quinone / Substrate / membrane protein / Escherichia coli / OXIDOREDUCTASE
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.23 Å
Authorsvan der Velden TT / Kayastha K / Bruenle S / Jeuken LJC
Funding support Netherlands, 1 items
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
DepositionJul 16, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54414.png

Downloads & links

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Map

FileDownload / File: emd_54414.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0364
Minimum - Maximum-0.20010544 - 0.4251147
Average (Standard dev.)0.00017562167 (±0.007525335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54414_msk_1.map
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Half map: #1

Fileemd_54414_half_map_1.map
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Half map: #2

Fileemd_54414_half_map_2.map
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Sample components

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Entire : E. coli cytochrome bd-I

EntireName: E. coli cytochrome bd-I
Components
  • Complex: E. coli cytochrome bd-I
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit X
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: MENAQUINONE-9
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: Ubiquinone-8
  • Ligand: OXYGEN MOLECULE
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: water

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Supramolecule #1: E. coli cytochrome bd-I

SupramoleculeName: E. coli cytochrome bd-I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Cytochrome bd-I ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: quinol oxidase (electrogenic, proton-motive force generating)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 58.251723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLDIVELSRL QFALTAMYHF LFVPLTLGMA FLLAIMETVY VLSGKQIYKD MTKFWGKLFG INFALGVATG LTMEFQFGTN WSYYSHYVG DIFGAPLAIE GLMAFFLEST FVGLFFFGWD RLGKVQHMCV TWLVALGSNL SALWILVANG WMQNPIASDF N FETMRMEM ...String:
MLDIVELSRL QFALTAMYHF LFVPLTLGMA FLLAIMETVY VLSGKQIYKD MTKFWGKLFG INFALGVATG LTMEFQFGTN WSYYSHYVG DIFGAPLAIE GLMAFFLEST FVGLFFFGWD RLGKVQHMCV TWLVALGSNL SALWILVANG WMQNPIASDF N FETMRMEM VSFSELVLNP VAQVKFVHTV ASGYVTGAMF ILGISAWYML KGRDFAFAKR SFAIAASFGM AAVLSVIVLG DE SGYEMGD VQKTKLAAIE AEWETQPAPA AFTLFGIPDQ EEETNKFAIQ IPYALGIIAT RSVDTPVIGL KELMVQHEER IRN GMKAYS LLEQLRSGST DQAVRDQFNS MKKDLGYGLL LKRYTPNVAD ATEAQIQQAT KDSIPRVAPL YFAFRIMVAC GFLL LAIIA LSFWSVIRNR IGEKKWLLRA ALYGIPLPWI AVEAGWFVAE YGRQPWAIGE VLPTAVANSS LTAGDLIFSM VLICG LYTL FLVAELFLMF KFARLGPSSL KTGRYHFEQS STTTQPAR

UniProtKB: Cytochrome bd-I ubiquinol oxidase subunit 1

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Macromolecule #2: Cytochrome bd-I ubiquinol oxidase subunit 2

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: quinol oxidase (electrogenic, proton-motive force generating)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 42.479828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI NSIAPHWDGN QVWLITAGGA LFAAWPMVYA AAFSGFYVA MILVLASLFF RPVGFDYRSK IEETRWRNMW DWGIFIGSFV PPLVIGVAFG NLLQGVPFNV DEYLRLYYTG N FFQLLNPF ...String:
MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI NSIAPHWDGN QVWLITAGGA LFAAWPMVYA AAFSGFYVA MILVLASLFF RPVGFDYRSK IEETRWRNMW DWGIFIGSFV PPLVIGVAFG NLLQGVPFNV DEYLRLYYTG N FFQLLNPF GLLAGVVSVG MIITQGATYL QMRTVGELHL RTRATAQVAA LVTLVCFALA GVWVMYGIDG YVVKSTMDHY AA SNPLNKE VVREAGAWLV NFNNTPILWA IPALGVVLPL LTILTARMDK AAWAFVFSSL TLACIILTAG IAMFPFVMPS STM MNASLT MWDATSSQLT LNVMTWVAVV LVPIILLYTA WCYWKMFGRI TKEDIERNTH SLY

UniProtKB: Cytochrome bd-I ubiquinol oxidase subunit 2

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Macromolecule #3: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 2.999651 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTDLKFSLV TTIIVLGLIV AVGLTAALH

UniProtKB: Uncharacterized protein YnhF

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Macromolecule #4: Cytochrome bd-I ubiquinol oxidase subunit X

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit X / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
EC number: quinol oxidase (electrogenic, proton-motive force generating)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 4.043663 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MWYFAWILGT LLACSFGVIT ALALEHVESG KAGQEDI

UniProtKB: Cytochrome bd-I ubiquinol oxidase subunit X

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #6: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 6 / Number of copies: 2 / Formula: A1JN4
Molecular weightTheoretical: 636.518 Da

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Macromolecule #7: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 7 / Number of copies: 4 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #8: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 8 / Number of copies: 6 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #9: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 9 / Number of copies: 2 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #10: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 10 / Number of copies: 2 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #11: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 11 / Number of copies: 4 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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Macromolecule #12: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 12 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 77 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 530094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

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

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