+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10049 | |||||||||
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Title | THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI | |||||||||
Map data | sharpened map after postprocess (Relion) without mask | |||||||||
Sample |
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Keywords | BD OXIDASE / TERMINAL OXIDASE / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information 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 / electron transfer activity / heme binding / membrane ...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 / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Rasmussen T / Boettcher B | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Homologous bd oxidases share the same architecture but differ in mechanism. Authors: Alexander Theßeling / Tim Rasmussen / Sabrina Burschel / Daniel Wohlwend / Jan Kägi / Rolf Müller / Bettina Böttcher / Thorsten Friedrich / Abstract: Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus ...Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10049.map.gz | 12.1 MB | EMDB map data format | |
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Header (meta data) | emd-10049-v30.xml emd-10049.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10049_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_10049.png | 212.2 KB | ||
Filedesc metadata | emd-10049.cif.gz | 6.8 KB | ||
Others | emd_10049_half_map_1.map.gz emd_10049_half_map_2.map.gz | 9.8 MB 9.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10049 | HTTPS FTP |
-Validation report
Summary document | emd_10049_validation.pdf.gz | 734.6 KB | Display | EMDB validaton report |
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Full document | emd_10049_full_validation.pdf.gz | 734.2 KB | Display | |
Data in XML | emd_10049_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_10049_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10049 | HTTPS FTP |
-Related structure data
Related structure data | 6rx4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10049.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map after postprocess (Relion) without mask | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: unfiltered half map
File | emd_10049_half_map_1.map | ||||||||||||
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Annotation | unfiltered half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map
File | emd_10049_half_map_2.map | ||||||||||||
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Annotation | unfiltered half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : bd-oxidase from Escherichia coli
+Supramolecule #1: bd-oxidase from Escherichia coli
+Macromolecule #1: Cytochrome bd-I ubiquinol oxidase subunit 1
+Macromolecule #2: Cytochrome bd-I ubiquinol oxidase subunit 2
+Macromolecule #3: Cytochrome bd-I ubiquinol oxidase subunit X
+Macromolecule #4: Cytochrome bd-I ubiquinol oxidase subunit Y
+Macromolecule #5: HEME B/C
+Macromolecule #6: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
+Macromolecule #7: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #8: Ubiquinone-8
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 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: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0029300000000000003 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3.5 sec, blot force 5. |
-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 / Number grids imaged: 1 / Number real images: 8663 / Average exposure time: 75.0 sec. / Average electron dose: 59.0 e/Å2 Details: Images were collected in movie mode with 47 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |