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- EMDB-10049: THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: EMDB / ID: EMD-10049
TitleTHE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI
Map datasharpened map after postprocess (Relion) without mask
Sample
  • Complex: bd-oxidase from Escherichia coli
    • 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 subunit X
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit Y
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: Ubiquinone-8Coenzyme Q10
  • Ligand: water
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 / electron transfer activity / heme binding / membrane ...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 / 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
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: 3.3 Å
AuthorsRasmussen T / Boettcher B / Thesseling A / Friedrich T
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nat Commun / Year: 2019
Title: Homologous bd oxidases share the same architecture but differ in mechanism.
Authors: Alexander Theßeling / Tim Rasmussen / Sabrina Burschel / Daniel Wohlwend / Jan Kägi / Rolf Müller / Bettina Böttcher / Thorsten Friedrich /
Abstract: Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus ...Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism.
History
DepositionJun 7, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseNov 20, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.052
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.052
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rx4
  • Surface level: 0.052
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10049.png

Downloads & links

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Map

FileDownload / File: emd_10049.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map after postprocess (Relion) without mask
Voxel sizeX=Y=Z: 1.0635 Å
Density
Contour LevelBy AUTHOR: 0.052 / Movie #1: 0.052
Minimum - Maximum-0.12678012 - 0.22499055
Average (Standard dev.)0.0017706004 (±0.011363435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 159.52501 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06351.06351.0635
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z159.525159.525159.525
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1270.2250.002

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Supplemental data

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Half map: unfiltered half map

Fileemd_10049_half_map_1.map
Annotationunfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map

Fileemd_10049_half_map_2.map
Annotationunfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : bd-oxidase from Escherichia coli

EntireName: bd-oxidase from Escherichia coli
Components
  • Complex: bd-oxidase from Escherichia coli
    • 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 subunit X
    • Protein or peptide: Cytochrome bd-I ubiquinol oxidase subunit Y
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: Ubiquinone-8Coenzyme Q10
  • Ligand: water

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Supramolecule #1: bd-oxidase from Escherichia coli

SupramoleculeName: bd-oxidase from Escherichia coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Reconstruction into Amphipole A8-35 in the presence of the inhibitor aurachin C.
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: 1 / Enantiomer: LEVO
EC number: quinol oxidase (electrogenic, proton-motive force generating)
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 58.251723 KDa
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

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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 (strain K12) (bacteria)
Molecular weightTheoretical: 42.479828 KDa
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

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Macromolecule #3: Cytochrome bd-I ubiquinol oxidase subunit X

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit X / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: quinol oxidase (electrogenic, proton-motive force generating)
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 4.043663 KDa
SequenceString:
MWYFAWILGT LLACSFGVIT ALALEHVESG KAGQEDI

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

MacromoleculeName: Cytochrome bd-I ubiquinol oxidase subunit Y / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 2.230741 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

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

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Macromolecule #7: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 749.073 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

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Macromolecule #8: Ubiquinone-8

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

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
20.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00293 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3.5 sec, blot force 5.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8663 / Average exposure time: 75.0 sec. / Average electron dose: 59.0 e/Å2
Details: Images were collected in movie mode with 47 frames.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 197805
DetailsMovies were motion corrected and dose weighted with the program Motioncorr2.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5doq

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 88
Output model

PDB-6rx4:
THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI

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