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Open data
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Basic information
Entry | Database: PDB / ID: 8f6c | ||||||
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Title | E. coli cytochrome bo3 ubiquinol oxidase dimer | ||||||
![]() | (Cytochrome bo(3) ubiquinol oxidase subunit ...) x 4 | ||||||
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Function / homology | ![]() cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, Y. / Karimullina, E. / Borek, D. / Savchenko, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 449 KB | Display | ![]() |
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PDB format | ![]() | 361.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28879MC ![]() 8f68C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Cytochrome bo(3) ubiquinol oxidase subunit ... , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 73896.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0ABI8, ![]() #2: Protein | Mass: 28839.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Protein | Mass: 20464.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #4: Protein | Mass: 10742.083 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 12 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/3PE.gif)
#5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-3PE / ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: E. coli Cytochrome bo3 ubiquinol oxidase dimer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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3D reconstruction![]() | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40700 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.46→146.78 Å / Cor.coef. Fo:Fc: 0.734 / SU B: 52.565 / SU ML: 0.717 / ESU R: 1.439 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 19344 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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