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- EMDB-13048: cytochrome bd-II type oxidase with bound aurachin D -

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Basic information

Entry
Database: EMDB / ID: EMD-13048
Titlecytochrome bd-II type oxidase with bound aurachin D
Map datapost-processed sharpened map
Sample
  • Complex: Cytochrome bd-II ubiquinol oxidase
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 2
    • Protein or peptide: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: Aurachin D
  • Ligand: Ubiquinone-8
  • Ligand: water
Keywordsterminal oxidase / Q-loop / inhibitor binding / MEMBRANE PROTEIN
Function / homology
Function and homology information


ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cell outer membrane / electron transfer activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
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
Putative cytochrome bd-II ubiquinol oxidase subunit AppX / Cytochrome bd-II ubiquinol oxidase subunit 2 / Cytochrome bd-II ubiquinol oxidase subunit 1
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGrauel A / Kaegi J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)278002225/RTG 2202 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D.
Authors: Antonia Grauel / Jan Kägi / Tim Rasmussen / Iryna Makarchuk / Sabrina Oppermann / Aurélien F A Moumbock / Daniel Wohlwend / Rolf Müller / Frederic Melin / Stefan Günther / Petra Hellwig ...Authors: Antonia Grauel / Jan Kägi / Tim Rasmussen / Iryna Makarchuk / Sabrina Oppermann / Aurélien F A Moumbock / Daniel Wohlwend / Rolf Müller / Frederic Melin / Stefan Günther / Petra Hellwig / Bettina Böttcher / Thorsten Friedrich /
Abstract: Cytochrome bd quinol:O oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria. Escherichia coli contains two bd oxidases of ...Cytochrome bd quinol:O oxidoreductases are respiratory terminal oxidases so far only identified in prokaryotes, including several pathogenic bacteria. Escherichia coli contains two bd oxidases of which only the bd-I type is structurally characterized. Here, we report the structure of the Escherichia coli cytochrome bd-II type oxidase with the bound inhibitor aurachin D as obtained by electron cryo-microscopy at 3 Å resolution. The oxidase consists of subunits AppB, C and X that show an architecture similar to that of bd-I. The three heme cofactors are found in AppC, while AppB is stabilized by a structural ubiquinone-8 at the homologous positions. A fourth subunit present in bd-I is lacking in bd-II. Accordingly, heme b is exposed to the membrane but heme d embedded within the protein and showing an unexpectedly high redox potential is the catalytically active centre. The structure of the Q-loop is fully resolved, revealing the specific aurachin binding.
History
DepositionJun 8, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ose
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13048.png

Downloads & links

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Map

FileDownload / File: emd_13048.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212.7 Å		1.06 Å/pix.
x 200 pix.
= 212.7 Å		1.06 Å/pix.
x 200 pix.
= 212.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.092141904 - 0.17856313
Average (Standard dev.)0.00033691214 (±0.009092562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 212.70001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06351.06351.0635
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.700212.700212.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0920.1790.000

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Supplemental data

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Sample components

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Entire : Cytochrome bd-II ubiquinol oxidase

EntireName: Cytochrome bd-II ubiquinol oxidase
Components
  • Complex: Cytochrome bd-II ubiquinol oxidase
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 2
    • Protein or peptide: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: Aurachin D
  • Ligand: Ubiquinone-8
  • Ligand: water

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Supramolecule #1: Cytochrome bd-II ubiquinol oxidase

SupramoleculeName: Cytochrome bd-II ubiquinol oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: dimer of heterotrimers solubilised in amphipol A8-35 in complex with the inhibitor Aurachin D
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 208 KDa

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

MacromoleculeName: Cytochrome bd-II ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting)
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 57.962469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWDVIDLSRW QFALTALYHF LFVPLTLGLI FLLAIMETIY VVTGKTIYRD MTRFWGKLFG INFALGVATG LTMEFQFGTN WSFYSNYVG DIFGAPLAME ALMAFFLEST FVGLFFFGWQ RLNKYQHLLV TWLVAFGSNL SALWILNANG WMQYPTGAHF D IDTLRMEM ...String:
MWDVIDLSRW QFALTALYHF LFVPLTLGLI FLLAIMETIY VVTGKTIYRD MTRFWGKLFG INFALGVATG LTMEFQFGTN WSFYSNYVG DIFGAPLAME ALMAFFLEST FVGLFFFGWQ RLNKYQHLLV TWLVAFGSNL SALWILNANG WMQYPTGAHF D IDTLRMEM TSFSELVFNP VSQVKFVHTV MAGYVTGAMF IMAISAWYLL RGRERNVALR SFAIGSVFGT LAIIGTLQLG DS SAYEVAQ VQPVKLAAME GEWQTEPAPA PFHVVAWPEQ DQERNAFALK IPALLGILAT HSLDKPVPGL KNLMAETYPR LQR GRMAWL LMQEISQGNR EPHVLQAFRG LEGDLGYGML LSRYAPDMNH VTAAQYQAAM RGAIPQVAPV FWSFRIMVGC GSLL LLVML IALVQTLRGK IDQHRWVLKM ALWSLPLPWI AIEAGWFMTE FGRQPWAIQD ILPTYSAHSA LTTGQLAFSL IMIVG LYTL FLIAEVYLMQ KYARLGPSAM QSEQPTQQQG

UniProtKB: Cytochrome bd-II ubiquinol oxidase subunit 1

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

MacromoleculeName: Cytochrome bd-II ubiquinol oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting)
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 42.448543 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFDYETLRFI WWLLIGVILV VFMISDGFDM GIGCLLPLVA RNDDERRIVI NSVGAHWEGN QVWLILAGGA LFAAWPRVYA AAFSGFYVA MILVLCSLFF RPLAFDYRGK IADARWRKMW DAGLVIGSLV PPVVFGIAFG NLLLGVPFAF TPQLRVEYLG S FWQLLTPF ...String:
MFDYETLRFI WWLLIGVILV VFMISDGFDM GIGCLLPLVA RNDDERRIVI NSVGAHWEGN QVWLILAGGA LFAAWPRVYA AAFSGFYVA MILVLCSLFF RPLAFDYRGK IADARWRKMW DAGLVIGSLV PPVVFGIAFG NLLLGVPFAF TPQLRVEYLG S FWQLLTPF PLLCGLLSLG MVILQGGVWL QLKTVGVIHL RSQLATKRAA LLVMLCFLLA GYWLWVGIDG FVLLAQDANG PS NPLMKLV AVLPGAWMNN FVESPVLWIF PLLGFFCPLL TVMAIYRGRP GWGFLMASLM QFGVIFTAGI TLFPFVMPSS VSP ISSLTL WDSTSSQLTL SIMLVIVLIF LPIVLLYTLW SYYKMWGRMT TETLRRNENE LY

UniProtKB: Cytochrome bd-II ubiquinol oxidase subunit 2

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Macromolecule #3: Putative cytochrome bd-II ubiquinol oxidase subunit AppX

MacromoleculeName: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria) / Strain: K12
Molecular weightTheoretical: 3.599463 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MWYLLWFVGI LLMCSLSTLV LVWLDPRLKS

UniProtKB: Putative cytochrome bd-II ubiquinol oxidase subunit AppX

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Macromolecule #4: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 4 / Number of copies: 4 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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Macromolecule #5: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 5 / Number of copies: 2 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

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

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Macromolecule #6: Aurachin D

MacromoleculeName: Aurachin D / type: ligand / ID: 6 / Number of copies: 2 / Formula: 0NI
Molecular weightTheoretical: 363.536 Da
Chemical component information

ChemComp-0NI:
Aurachin D

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Macromolecule #7: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 7 / Number of copies: 2 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 2 / 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

Concentration5.6 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
20.0 mMNaClsodium chloride
160.0 uMC25H33NOAurachin D
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 45 sec incubation, 6.5 sec blotting.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1836 / Average exposure time: 75.0 sec. / Average electron dose: 79.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 75000
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: 800000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 125497
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6rx4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 94 / Target criteria: WEIGHTED MAP SUM AT ATOM CENTERS
Output model

PDB-7ose:
cytochrome bd-II type oxidase with bound aurachin D

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