+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40625 | |||||||||
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Title | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa | |||||||||
Map data | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (composite structure) | |||||||||
Sample |
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Keywords | Electron transport chain / Supercomplex / Pseudomonas aeruginosa / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain ...cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Di Trani JM / Rubinstein JL | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structure of the - respiratory supercomplex from . Authors: Justin M Di Trani / Andreea A Gheorghita / Madison Turner / Peter Brzezinski / Pia Ädelroth / Siavash Vahidi / P Lynne Howell / John L Rubinstein / Abstract: Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that ...Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that enables ATP synthesis and membrane transport. These protein complexes can also form higher order assemblies known as respiratory supercomplexes (SCs). The electron transport chain of the opportunistic pathogen is closely linked with its ability to invade host tissue, tolerate harsh conditions, and resist antibiotics but is poorly characterized. Here, we determine the structure of a SC that forms between the quinol:cytochrome oxidoreductase (cytochrome ) and one of the organism's terminal oxidases, cytochrome , which is found only in some bacteria. Remarkably, the SC structure also includes two intermediate electron carriers: a diheme cytochrome and a single heme cytochrome . Together, these proteins allow electron transfer from ubiquinol in cytochrome to oxygen in cytochrome . We also present evidence that different isoforms of cytochrome can participate in formation of this SC without changing the overall SC architecture. Incorporating these different subunit isoforms into the SC would allow the bacterium to adapt to different environmental conditions. Bioinformatic analysis focusing on structural motifs in the SC suggests that cytochrome - SCs also exist in other bacterial pathogens. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40625.map.gz | 106.9 MB | EMDB map data format | |
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Header (meta data) | emd-40625-v30.xml emd-40625.xml | 30.7 KB 30.7 KB | Display Display | EMDB header |
Images | emd_40625.png | 117.8 KB | ||
Filedesc metadata | emd-40625.cif.gz | 7.5 KB | ||
Others | emd_40625_additional_1.map.gz emd_40625_additional_2.map.gz emd_40625_additional_3.map.gz emd_40625_half_map_1.map.gz emd_40625_half_map_2.map.gz | 131.8 MB 66.4 MB 70.2 MB 129.7 MB 129.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40625 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40625 | HTTPS FTP |
-Related structure data
Related structure data | 8snhMC 8smrC 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_40625.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (composite structure) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
File | emd_40625_additional_1.map | ||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...
File | emd_40625_additional_2.map | ||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, locally sharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...
File | emd_40625_additional_3.map | ||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, unsharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map...
File | emd_40625_half_map_1.map | ||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map...
File | emd_40625_half_map_2.map | ||||||||||||
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Annotation | cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map B) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : cytochrome bc1-cbb3 supercomplex
+Supramolecule #1: cytochrome bc1-cbb3 supercomplex
+Macromolecule #1: cytochrome-c oxidase
+Macromolecule #2: Ubiquinol-cytochrome c reductase iron-sulfur subunit
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1
+Macromolecule #5: Cytochrome c4
+Macromolecule #6: Cytochrome C5
+Macromolecule #7: Cbb3-type Cytochrome C oxidase subunit II
+Macromolecule #8: Cbb3-type cytochrome c oxidase subunit
+Macromolecule #9: COPPER (II) ION
+Macromolecule #10: CALCIUM ION
+Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #12: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #13: (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl ...
+Macromolecule #14: UBIQUINONE-10
+Macromolecule #15: HEME C
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48594 |