+Open data
-Basic information
Entry | Database: PDB / ID: 8f68 | ||||||
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Title | E. coli cytochrome bo3 ubiquinol oxidase monomer | ||||||
Components | (Cytochrome bo(3) ubiquinol oxidase subunit ...) x 4 | ||||||
Keywords | PROTON TRANSPORT / heme-copper oxidase / proton translocation / E. coli aerobic respiratory chain / membrane protein | ||||||
Function / homology | Function and homology information oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / proton transmembrane transporter activity / electron transport coupled proton transport ...oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / proton transmembrane transporter activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Guo, Y. / Karimullina, E. / Borek, D. / Savchenko, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci / Year: 2023 Title: Monomer and dimer structures of cytochrome bo ubiquinol oxidase from Escherichia coli. Authors: Yirui Guo / Elina Karimullina / Tabitha Emde / Zbyszek Otwinowski / Dominika Borek / Alexei Savchenko / Abstract: The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it ...The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts-the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74). | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f68.cif.gz | 243.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f68.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 8f68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f68_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8f68_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8f68_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 8f68_validation.cif.gz | 67.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/8f68 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/8f68 | HTTPS FTP |
-Related structure data
Related structure data | 28877MC 8f6cC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome bo(3) ubiquinol oxidase subunit ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 73896.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoB, b0431, JW0421 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABI8, ubiquinol oxidase (H+-transporting) |
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#2: Protein | Mass: 28839.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoA, b0432, JW0422 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ1 |
#3: Protein | Mass: 20464.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoC, b0430, JW0420 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ3 |
#4: Protein | Mass: 10660.987 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoD, b0429, JW0419 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ6 |
-Non-polymers , 4 types, 6 molecules
#5: Chemical | ChemComp-HEM / |
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#6: Chemical | ChemComp-HEO / |
#7: Chemical | ChemComp-CU / |
#8: Chemical |
-Details
Has ligand of interest | Y |
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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: E. coli Cytochrome bo3 ubiquinol oxidase monomer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150028 / Symmetry type: POINT |