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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22447 | |||||||||
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Title | Plant Mitochondrial complex IV from Vigna radiata | |||||||||
![]() | Plant Mitochondrial complex IV from Vigna radiata | |||||||||
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Function / homology | ![]() respiratory chain complex IV / : / : / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / : / mitochondrial inner membrane / membrane => GO:0016020 / copper ion binding / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Maldonado M / Letts JA | |||||||||
![]() | ![]() Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants. Authors: Maria Maldonado / Fei Guo / James A Letts / ![]() Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses. | |||||||||
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 | ![]() | 480.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.3 KB 29.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.2 KB | Display | ![]() |
Images | ![]() | 84.6 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() | 411.5 MB 411.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 862.1 KB | Display | ![]() |
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Full document | ![]() | 861.7 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jroMC ![]() 7jrgC ![]() 7jrpC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 6.7 TB Data #1: Raw movies of mixed sample used for determination of mung bean respiratory CI*, CIII2, CIV and SC III2+IV [micrographs - multiframe]) |
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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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Annotation | Plant Mitochondrial complex IV from Vigna radiata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Plant Mitochondrial complex IV from Vigna radiata. Half map 1.
File | emd_22447_half_map_1.map | ||||||||||||
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Annotation | Plant Mitochondrial complex IV from Vigna radiata. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Plant Mitochondrial complex IV from Vigna radiata. Half map 2.
File | emd_22447_half_map_2.map | ||||||||||||
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Annotation | Plant Mitochondrial complex IV from Vigna radiata. Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Mitochondrial Respiratory Complex IV
+Supramolecule #1: Mitochondrial Respiratory Complex IV
+Macromolecule #1: COX1
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: COX3
+Macromolecule #4: COX4
+Macromolecule #5: cytochrome c oxidase subunit 5b-2, mitochondrial
+Macromolecule #6: cytochrome c oxidase subunit 6a, mitochondrial
+Macromolecule #7: cytochrome c oxidase subunit 6b-1
+Macromolecule #8: Cytochrome c oxidase subunit 5C
+Macromolecule #9: COX7a
+Macromolecule #10: COX7c
+Macromolecule #11: HEME-A
+Macromolecule #12: COPPER (II) ION
+Macromolecule #13: MAGNESIUM ION
+Macromolecule #14: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #15: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #16: CARDIOLIPIN
+Macromolecule #17: DINUCLEAR COPPER ION
+Macromolecule #18: ZINC ION
+Macromolecule #19: LYSINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III | |||||||||||||||
Details | This sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 60010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |