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- EMDB-13777: III2-IV2 respiratory supercomplex from Corynebacterium glutamicum -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13777 | |||||||||||||||
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Title | III2-IV2 respiratory supercomplex from Corynebacterium glutamicum | |||||||||||||||
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Function / homology | ![]() aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / respirasome / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / respirasome / electron transport coupled proton transport / ATP synthesis coupled electron 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 | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
![]() | Kovalova T / Moe A / Krol S / Yanofsky DJ / Bott M / Sjostrand D / Rubinstein JL / Hogbom M / Brzezinski P | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The respiratory supercomplex from C. glutamicum. Authors: Agnes Moe / Terezia Kovalova / Sylwia Król / David J Yanofsky / Michael Bott / Dan Sjöstrand / John L Rubinstein / Martin Högbom / Peter Brzezinski / ![]() ![]() ![]() Abstract: Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, ...Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, respiratory complexes III and IV form a CIIICIV supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 Å resolution. The structure shows a central CIII dimer flanked by a CIV on two sides. A menaquinone is bound in each of the Q and Q sites in each CIII and an additional menaquinone is positioned ∼14 Å from heme b. A di-heme cyt. cc subunit electronically connects each CIII with an adjacent CIV, with the Rieske iron-sulfur protein positioned with the iron near heme b. Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a path for proton transfer into CIV. | |||||||||||||||
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 | ![]() | 9.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.1 KB 35.1 KB | Display Display | ![]() |
Images | ![]() | 89.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 322 KB | Display | ![]() |
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Full document | ![]() | 321.6 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q21MC 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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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 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 : The respiratory supercomplex
+Supramolecule #1: The respiratory supercomplex
+Macromolecule #1: Co-purified unknown transmembrane helices built as polyALA (AscD)
+Macromolecule #2: Cytochrome c oxidase subunit 3
+Macromolecule #3: Uncharacterized membrane protein Cgl2017/cg2211
+Macromolecule #4: Cytochrome c oxidase polypeptide 4
+Macromolecule #5: Cytochrome c oxidase subunit 2
+Macromolecule #6: Cytochrome c oxidase subunit 1
+Macromolecule #7: Cytochrome bc1 complex Rieske iron-sulfur subunit
+Macromolecule #8: Uncharacterized protein Cgl2664/cg2949
+Macromolecule #9: Cytochrome bc1 complex cytochrome b subunit
+Macromolecule #10: Cytochrome bc1 complex cytochrome c subunit
+Macromolecule #11: Co-purified unknown peptide built as polyALA (AscE)
+Macromolecule #12: Co-purified unknown peptide built as polyALA (AscE)
+Macromolecule #13: Actinobacterial supercomplex, subunit C (AscC)
+Macromolecule #14: Hypothetical membrane protein
+Macromolecule #15: CARDIOLIPIN
+Macromolecule #16: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
+Macromolecule #17: TRIDECANE
+Macromolecule #18: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
+Macromolecule #19: DOCOSANE
+Macromolecule #20: COPPER (II) ION
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: HEME-AS
+Macromolecule #23: CALCIUM ION
+Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #25: MENAQUINONE-9
+Macromolecule #26: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...
+Macromolecule #27: PALMITIC ACID
+Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #29: HEME C
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-2/2 / 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: 276 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65391 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |