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- EMDB-4908: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4908
TitleCryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution
Map data
Sample
  • Complex: Cytochrome bd-I oxidase from E. coli
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 1
    • Protein or peptide: Uncharacterized protein YnhF
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit X
  • Ligand: Ubiquinone-8
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C
  • Ligand: OXYGEN MOLECULE
  • Ligand: water
KeywordsOxidoreductase Cytochrome bd oxidase bd oxidase Oxidase / MEMBRANE PROTEIN
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 / metal ion binding / membrane / 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) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsSafarian S / Hahn A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Science / Year: 2019
Title: Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.
Authors: S Safarian / A Hahn / D J Mills / M Radloff / M L Eisinger / A Nikolaev / J Meier-Credo / F Melin / H Miyoshi / R B Gennis / J Sakamoto / J D Langer / P Hellwig / W Kühlbrandt / H Michel /
Abstract: Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial ...Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the cytochrome bd-I oxidase by single-particle cryo-electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.
History
DepositionApr 30, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseOct 16, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rko
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4908.png

Downloads & links

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Map

FileDownload / File: emd_4908.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.67130756 - 0.9967307
Average (Standard dev.)0.00014172592 (±0.016276969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.6710.9970.000

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Supplemental data

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Sample components

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Entire : Cytochrome bd-I oxidase from E. coli

EntireName: Cytochrome bd-I oxidase from E. coli
Components
  • Complex: Cytochrome bd-I oxidase from E. coli
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit 1
    • Protein or peptide: Uncharacterized protein YnhF
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit X
  • Ligand: Ubiquinone-8
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C
  • Ligand: OXYGEN MOLECULE
  • Ligand: water

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Supramolecule #1: Cytochrome bd-I oxidase from E. coli

SupramoleculeName: Cytochrome bd-I oxidase from E. coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 107.7 KDa

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Macromolecule #1: Cytochrome bd-I ubiquinol oxidase subunit 2

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit 2 / 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 (strain K12) (bacteria) / Strain: K12
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 #2: Cytochrome bd-I ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit 1 / 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 (strain K12) (bacteria) / Strain: K12
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 #3: Uncharacterized protein YnhF

MacromoleculeName: Uncharacterized protein YnhF / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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 (strain K12) (bacteria) / Strain: K12
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: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 5 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #6: (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: 6 / 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 #7: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 7 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

ChemComp-HDD:
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

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Macromolecule #8: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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Macromolecule #9: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 9 / Number of copies: 1 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 31 / 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

Concentration7 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
100.0 mMSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5463 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3500000
Startup modelType of model: INSILICO MODEL / In silico model: Relion3 initial model
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 170000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 120 / Target criteria: Cross-correlation coefficient
Output model

PDB-6rko:
Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

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