+Open data
-Basic information
Entry | Database: PDB / ID: 7ose | ||||||
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Title | cytochrome bd-II type oxidase with bound aurachin D | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / terminal oxidase / Q-loop / inhibitor binding | ||||||
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 / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli BW25113 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Grauel, A. / Kaegi, J. / Rasmussen, T. / Wohlwend, D. / Boettcher, B. / Friedrich, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ose.cif.gz | 333.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ose.ent.gz | 269.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ose.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7ose ftp://data.pdbj.org/pub/pdb/validation_reports/os/7ose | HTTPS FTP |
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-Related structure data
Related structure data | 13048MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome bd-II ubiquinol oxidase subunit ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 57962.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DeltacyoABCD References: UniProt: P26459, ubiquinol oxidase (H+-transporting) #2: Protein | Mass: 42448.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: appB, cbdB, cyxB, b0979, JW0961 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DeltacyoABCD References: UniProt: P26458, ubiquinol oxidase (H+-transporting) |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 3599.463 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Strain: K12 / Gene: appX, yccB, b4592, JW0961.1, b0979.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DeltacyoABCD / References: UniProt: P24244 |
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-Non-polymers , 5 types, 12 molecules
#4: Chemical | ChemComp-HEB / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cytochrome bd-II ubiquinol oxidase / Type: COMPLEX Details: dimer of heterotrimers solubilised in amphipol A8-35 in complex with the inhibitor Aurachin D Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.208 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli BW25113 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 45 sec incubation, 6.5 sec blotting |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 75 sec. / Electron dose: 79 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1836 |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 800000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125497 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 94 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: WEIGHTED MAP SUM AT ATOM CENTERS | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RX4 Accession code: 6RX4 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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