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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11924 | |||||||||
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Title | Cytochrome c oxidase structure in F-state | |||||||||
![]() | density modified map | |||||||||
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Function / homology | ![]() aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / copper ion binding / heme binding ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
![]() | Kolbe F / Safarian S / Michel H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase. Authors: F Kolbe / S Safarian / Ż Piórek / S Welsch / H Müller / H Michel / ![]() Abstract: Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) ...Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.8 KB 23.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 9.2 KB 7.6 KB | Display Display | ![]() |
Images | ![]() | 244.4 KB | ||
Others | ![]() ![]() ![]() | 57 MB 55.2 MB 55.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 423.3 KB | Display | ![]() |
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Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7au3MC ![]() 7ateC ![]() 7atnC ![]() 7au6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | density modified map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: relion postprocess map
File | emd_11924_additional_1.map | ||||||||||||
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Annotation | relion postprocess map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: relion half map 2
File | emd_11924_half_map_1.map | ||||||||||||
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Annotation | relion half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: relion half map 2
File | emd_11924_half_map_2.map | ||||||||||||
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Annotation | relion half map 2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Cytochrome c oxidase with four subunits reconstituted in lipid na...
+Supramolecule #1: Cytochrome c oxidase with four subunits reconstituted in lipid na...
+Macromolecule #1: Cytochrome c oxidase subunit 1-beta
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: Cytochrome c oxidase subunit 3
+Macromolecule #4: Cytochrome c oxidase subunit 4
+Macromolecule #5: MANGANESE (II) ION
+Macromolecule #6: HEME-A
+Macromolecule #7: COPPER (II) ION
+Macromolecule #8: CALCIUM ION
+Macromolecule #9: OXYGEN ATOM
+Macromolecule #10: SUPEROXO ION
+Macromolecule #11: DINUCLEAR COPPER ION
+Macromolecule #12: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 50.0 mM / Component - Formula: KPi / Component - Name: Potassium Phosphate |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 seconds before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 30.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |