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- PDB-7cuq: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichi... -
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Basic information
Entry | Database: PDB / ID: 7cuq | ||||||
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Title | 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane | ||||||
![]() | (Cytochrome bo(3) ubiquinol oxidase subunit ...) x 4 | ||||||
![]() | OXIDOREDUCTASE / proton pump / ubiquinol / oxidase | ||||||
Function / homology | ![]() cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / 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 / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / 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 / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / aerobic respiration / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | ||||||
![]() | Li, J. / Han, L. / Gennis, R.B. / Zhu, J.P. / Zhang, K. | ||||||
![]() | ![]() Title: Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Authors: Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis / ![]() ![]() Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98. | ||||||
History |
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Structure visualization
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PDBx/mmCIF format | ![]() | 229.8 KB | Display | ![]() |
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PDB format | ![]() | 180.3 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 58.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30474MC ![]() 7cubC ![]() 7cuwC ![]() 7n9zC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Cytochrome bo(3) ubiquinol oxidase subunit ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 74424.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P0ABI8, ubiquinol oxidase (H+-transporting) |
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#2: Protein | Mass: 32249.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 22642.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 12037.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 5 types, 9 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/UQ8.gif)
#5: Chemical | ChemComp-HEM / | ||
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#6: Chemical | ChemComp-HEO / | ||
#7: Chemical | ChemComp-CU / | ||
#8: Chemical | ChemComp-3PE / #9: Chemical | ChemComp-UQ8 / | |
-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 |
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Sample preparation
Component | Name: Cytochrome bo(3) ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Molecular weight | Value: 0.14 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 1.3 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: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209984 / Symmetry type: POINT |