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Yorodumi- EMDB-22450: Plant mitochondrial complex III2 from Vigna radiata supercomplex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22450 | |||||||||
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Title | Plant mitochondrial complex III2 from Vigna radiata supercomplex III2+IV, focused refinement. | |||||||||
Map data | Plant mitochondrial CIII2 focused map from Vigna radiata SC III2 IV. | |||||||||
Sample |
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Function / homology | Function and homology information mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / heme binding ...mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | Vigna radiata (mung bean) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Maldonado M / Guo F / Letts JA | |||||||||
Citation | Journal: Elife / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22450.map.gz | 480.4 MB | EMDB map data format | |
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Header (meta data) | emd-22450-v30.xml emd-22450.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22450_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_22450.png | 90.6 KB | ||
Masks | emd_22450_msk_1.map | 512 MB | Mask map | |
Others | emd_22450_half_map_1.map.gz emd_22450_half_map_2.map.gz | 410.3 MB 410.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22450 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22450 | HTTPS FTP |
-Related structure data
Related structure data | 7jrgC 7jroC 7jrpC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10586 (Title: Cryo electron micrographs of digitonin-solubilized, amphipol-stabilized, sucrose-gradient-purified V. radiata mitochondrial membranes - mixed fraction containing CI*, CIII2 and SC III2+IV 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22450.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Plant mitochondrial CIII2 focused map from Vigna radiata SC III2 IV. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_22450_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Plant mitochondrial CIII2 focused map from Vigna radiata...
File | emd_22450_half_map_1.map | ||||||||||||
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Annotation | Plant mitochondrial CIII2 focused map from Vigna radiata SC III2 IV. Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Plant mitochondrial CIII2 focused map from Vigna radiata...
File | emd_22450_half_map_2.map | ||||||||||||
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Annotation | Plant mitochondrial CIII2 focused map from Vigna radiata SC III2 IV. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plant mitochondrial complex III2
Entire | Name: Plant mitochondrial complex III2 |
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Components |
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-Supramolecule #1: Plant mitochondrial complex III2
Supramolecule | Name: Plant mitochondrial complex III2 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Vigna radiata (mung bean) / Tissue: hypocotyl / Organelle: mitochondria |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |