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- EMDB-4908: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4908 | |||||||||
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Title | Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution | |||||||||
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![]() | Oxidoreductase Cytochrome bd oxidase bd oxidase Oxidase / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() quinol oxidase (electrogenic, proton-motive force generating) / oxidoreductase activity, acting on diphenols and related substances as donors / cytochrome complex / aerobic electron transport chain / outer membrane / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cellular response to hypoxia / membrane => GO:0016020 / electron transfer activity ...quinol oxidase (electrogenic, proton-motive force generating) / oxidoreductase activity, acting on diphenols and related substances as donors / cytochrome complex / aerobic electron transport chain / outer membrane / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cellular response to hypoxia / membrane => GO:0016020 / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
![]() | Safarian S / Hahn A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Active site rearrangement and structural divergence in prokaryotic respiratory oxidases. Authors: S Safarian / A Hahn / D J Mills / M Radloff / M L Eisinger / A Nikolaev / J Meier-Credo / F Melin / H Miyoshi / R B Gennis / J Sakamoto / J D Langer / P Hellwig / W Kühlbrandt / H Michel / ![]() ![]() ![]() ![]() Abstract: Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial ...Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the cytochrome bd-I oxidase by single-particle cryo-electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site. | |||||||||
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 | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.5 KB 20.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 118.5 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 391.3 KB | Display | ![]() |
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Full document | ![]() | 390.9 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rkoMC 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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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Cytochrome bd-I oxidase from E. coli
+Supramolecule #1: Cytochrome bd-I oxidase from E. coli
+Macromolecule #1: Cytochrome bd-I ubiquinol oxidase subunit 2
+Macromolecule #2: Cytochrome bd-I ubiquinol oxidase subunit 1
+Macromolecule #3: Uncharacterized protein YnhF
+Macromolecule #4: Cytochrome bd-I ubiquinol oxidase subunit X
+Macromolecule #5: Ubiquinone-8
+Macromolecule #6: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+Macromolecule #7: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
+Macromolecule #8: HEME B/C
+Macromolecule #9: OXYGEN MOLECULE
+Macromolecule #10: 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 | 7 mg/mL | ||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5463 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 120 / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-6rko: |