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- EMDB-54801: E. coli cytochrome bd-I monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-54801
TitleE. coli cytochrome bd-I monomer
Map data
Sample
  • Complex: E.coli cytochrome bd-I
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit X
  • Ligand: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: OXYGEN MOLECULE
  • Ligand: Ubiquinone-8
  • Ligand: water
KeywordsRespiration / Complex / Cytochrome / 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
: / Membrane protein YnhF-like / 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 (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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
DepositionAug 15, 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_54801.png

Downloads & links

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Map

FileDownload / File: emd_54801.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0619
Minimum - Maximum-0.3561024 - 0.5548993
Average (Standard dev.)0.00002301223 (±0.008304698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54801_msk_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54801_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_54801_half_map_2.map
Projections & Slices
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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 2
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit X
  • Ligand: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: OXYGEN MOLECULE
  • Ligand: Ubiquinone-8
  • 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: #2, #1, #3-#4
Source (natural)Organism: Escherichia coli (E. coli)

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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: 1 / 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: 1 / 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: 1 / 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: 1 / 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: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1JN4
Molecular weightTheoretical: 636.518 Da

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Macromolecule #6: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #7: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 7 / Number of copies: 2 / 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 #8: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 8 / Number of copies: 1 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #9: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 9 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 32 / 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: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 200 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: 0.8 µm / Nominal magnification: 130000

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rko

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 399575
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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