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Yorodumi- EMDB-17210: Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17210 | |||||||||
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Title | Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RESPIRATORY SUPERCOMPLEX / MEMBRANE PROTEIN / ACTINOBACTERIA / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information aerobic electron transport chain / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / : ...aerobic electron transport chain / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / : / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Kovalova T / Krol S / Sjostrand D / Riepl D / Gamiz-Hernandez A / Brzezinski P / Kaila V / Hogbom M | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Long-range charge transfer mechanism of the IIIIV mycobacterial supercomplex. Authors: Daniel Riepl / Ana P Gamiz-Hernandez / Terezia Kovalova / Sylwia M Król / Sophie L Mader / Dan Sjöstrand / Martin Högbom / Peter Brzezinski / Ville R I Kaila / Abstract: Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing ...Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa IIIIV obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17210.map.gz | 567.7 MB | EMDB map data format | |
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Header (meta data) | emd-17210-v30.xml emd-17210.xml | 37.5 KB 37.5 KB | Display Display | EMDB header |
Images | emd_17210.png | 96 KB | ||
Filedesc metadata | emd-17210.cif.gz | 9.6 KB | ||
Others | emd_17210_half_map_1.map.gz emd_17210_half_map_2.map.gz | 557.6 MB 557.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17210 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17210 | HTTPS FTP |
-Validation report
Summary document | emd_17210_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_17210_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_17210_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_17210_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17210 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17210 | HTTPS FTP |
-Related structure data
Related structure data | 8ovcMC 8ovdC 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_17210.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17210_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17210_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The respiratory supercomplex
+Supramolecule #1: The respiratory supercomplex
+Macromolecule #1: Cytochrome bc1 complex cytochrome c subunit
+Macromolecule #2: Cytochrome bc1 complex cytochrome c subunit
+Macromolecule #3: Cytochrome bc1 complex cytochrome b subunit
+Macromolecule #4: Transmembrane protein
+Macromolecule #5: Probable cytochrome c oxidase subunit 3
+Macromolecule #6: Cytochrome c oxidase polypeptide 4
+Macromolecule #7: Cytochrome c oxidase subunit 1
+Macromolecule #8: cytochrome-c oxidase
+Macromolecule #9: Cytochrome c oxidase subunit
+Macromolecule #10: Uncharacterized protein MSMEG_4692/MSMEI_4575
+Macromolecule #11: LpqE protein
+Macromolecule #12: Superoxide dismutase [Cu-Zn]
+Macromolecule #13: Co-purified unknown peptide
+Macromolecule #14: Co-purified unknown peptide
+Macromolecule #15: HEME C
+Macromolecule #16: MENAQUINONE-9
+Macromolecule #17: acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
+Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #19: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...
+Macromolecule #20: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #21: CARDIOLIPIN
+Macromolecule #22: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
+Macromolecule #23: HEME-A
+Macromolecule #24: COPPER (II) ION
+Macromolecule #25: MAGNESIUM ION
+Macromolecule #26: CALCIUM ION
+Macromolecule #27: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
+Macromolecule #28: PALMITIC ACID
+Macromolecule #29: water
-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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Grid | Model: Quantifoil R2/2 / Material: COPPER / 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 III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.v) / Number images used: 90918 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |