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- PDB-7deg: Cryo-EM structure of a heme-copper terminal oxidase dimer provide... -
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Basic information
Entry | Database: PDB / ID: 7deg | ||||||
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Title | Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism | ||||||
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![]() | OXIDOREDUCTASE / electron cryo-microscopy / heme-copper oxidase / cytochrome c oxidase dimer / Aquifex aeolicus / naphthoquinone | ||||||
Function / homology | ![]() cytochrome-c oxidase activity / respirasome / aerobic respiration / membrane => GO:0016020 / copper ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Fei, S. / Hartmut, M. / Yun, Z. / Guoliang, Z. / Shuangbo, Z. | ||||||
![]() | ![]() Title: The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Authors: Guoliang Zhu / Hui Zeng / Shuangbo Zhang / Jana Juli / Linhua Tai / Danyang Zhang / Xiaoyun Pang / Yan Zhang / Sin Man Lam / Yun Zhu / Guohong Peng / Hartmut Michel / Fei Sun / ![]() ![]() Abstract: The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family ...The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.4 KB | Display | ![]() |
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PDB format | ![]() | 240.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 69.9 KB | Display | |
Data in CIF | ![]() | 94.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30657MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 65861.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome oxidase subunit ... , 2 types, 4 molecules CFBE
#2: Protein/peptide | Mass: 3944.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 16479.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 7 types, 18 molecules ![](data/chem/img/HAS.gif)
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![](data/chem/img/CU.gif)
![](data/chem/img/DLX.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/DLX.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CUA.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PGV / ( #9: Chemical | #10: Chemical | |
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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 |
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Sample preparation
Component | Name: cytochrome c oxidase (respiratory complex IV) / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1.5 mg/ml / 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: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32982 / Symmetry type: POINT |