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Yorodumi- EMDB-18594: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assemb... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18594 | ||||||||||||
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Title | Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs | ||||||||||||
Map data | Map sharpened by LocSpiral | ||||||||||||
Sample |
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Keywords | E. coli / membrane protein / Ni-NTA resin / cytochrome bo3 quinol oxidase / ubiquinone-8 release / peptidisc / single particle analysis / cryo-EM | ||||||||||||
Function / homology | Function and homology information 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 / ubiquinone binding / proton transmembrane transporter activity / 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 / ubiquinone binding / proton transmembrane transporter activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Gao Y / Zhang Y / Hakke S / Peters PJ / Ravelli RBG | ||||||||||||
Funding support | Netherlands, 3 items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2024 Title: Cryo-EM structure of cytochrome bo quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release. Authors: Ye Gao / Yue Zhang / Sneha Hakke / Ronny Mohren / Lyanne J P M Sijbers / Peter J Peters / Raimond B G Ravelli / Abstract: Cytochrome bo quinol oxidase belongs to the heme‑copper-oxidoreductase (HCO) superfamily, which is part of the respiratory chain and essential for cell survival. While the reaction mechanism of cyt ...Cytochrome bo quinol oxidase belongs to the heme‑copper-oxidoreductase (HCO) superfamily, which is part of the respiratory chain and essential for cell survival. While the reaction mechanism of cyt bo has been studied extensively over the last decades, specific details about its substrate binding and product release have remained unelucidated due to the lack of structural information. Here, we report a 2.8 Å cryo-electron microscopy structure of cyt bo from Escherichia coli assembled in peptidiscs. Our structural model shows a conformation for amino acids 1-41 of subunit I different from all previously published structures while the remaining parts of this enzyme are similar. Our new conformation shows a "U-shape" assembly in contrast to the transmembrane helix, named "TM0", in other reported structural models. However, TM0 blocks ubiquinone-8 (reaction product) release, suggesting that other cyt bo conformations should exist. Our structural model presents experimental evidence for an "open" conformation to facilitate substrate/product exchange. This work helps further understand the reaction cycle of this oxidase, which could be a benefit for potential drug/antibiotic design for health science. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18594.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-18594-v30.xml emd-18594.xml | 24 KB 24 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18594_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_18594.png | 114.2 KB | ||
Masks | emd_18594_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-18594.cif.gz | 7.3 KB | ||
Others | emd_18594_half_map_1.map.gz emd_18594_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18594 | HTTPS FTP |
-Validation report
Summary document | emd_18594_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_18594_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_18594_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_18594_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18594 | HTTPS FTP |
-Related structure data
Related structure data | 8qqkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18594.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Map sharpened by LocSpiral | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18594_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18594_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18594_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cytochrome bo3 quinol oxidase
+Supramolecule #1: Cytochrome bo3 quinol oxidase
+Macromolecule #1: Cytochrome bo(3) ubiquinol oxidase subunit 1
+Macromolecule #2: Cytochrome bo(3) ubiquinol oxidase subunit 2
+Macromolecule #3: Cytochrome bo(3) ubiquinol oxidase subunit 3
+Macromolecule #4: Cytochrome bo(3) ubiquinol oxidase subunit 4
+Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+Macromolecule #6: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #8: HEME O
+Macromolecule #9: COPPER (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: 20mM Tris-HCL, 150mM NaCl, 2% Glycerol, filtered and degassed. | ||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8050 / Average exposure time: 2.1 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |