[English] 日本語
![](img/lk-miru.gif)
- EMDB-22448: Plant Mitochondrial complex SC III2+IV from Vigna radiata composi... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-22448 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Plant Mitochondrial complex SC III2+IV from Vigna radiata composite map | |||||||||
![]() | Plant mitochondrial supercomplex III2 IV from Vigna radiata. Composite map. | |||||||||
![]() |
| |||||||||
Function / homology | ![]() protein processing involved in protein targeting to mitochondrion / respiratory chain complex IV / : / : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...protein processing involved in protein targeting to mitochondrion / respiratory chain complex IV / : / : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 / electron transfer activity / copper ion binding / heme binding / mitochondrion / proteolysis / metal ion binding 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 450.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 35.3 KB 35.3 KB | Display Display | ![]() |
Images | ![]() | 100.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 501.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 500.9 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jrpMC ![]() 7jrgC ![]() 7jroC M: atomic model generated by this map C: citing same article ( |
---|---|
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]) |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Plant mitochondrial supercomplex III2 IV from Vigna radiata. Composite map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Mitochondrial Respiratory Complex III2
+Supramolecule #1: Mitochondrial Respiratory Complex III2
+Macromolecule #1: Mitochondrial-processing peptidase subunit beta, mitochondrial is...
+Macromolecule #2: Alpha-MPP
+Macromolecule #3: COB
+Macromolecule #4: cytochrome c1-2, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7
+Macromolecule #7: cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6
+Macromolecule #9: cytochrome b-c1 complex subunit 9
+Macromolecule #10: QCR10
+Macromolecule #11: COX1
+Macromolecule #12: Cytochrome c oxidase subunit 2
+Macromolecule #13: COX3
+Macromolecule #14: COX4
+Macromolecule #15: cytochrome c oxidase subunit 5b-2, mitochondrial
+Macromolecule #16: cytochrome c oxidase subunit 6a, mitochondrial
+Macromolecule #17: cytochrome c oxidase subunit 6b-1
+Macromolecule #18: Cytochrome c oxidase subunit 5C
+Macromolecule #19: COX7a
+Macromolecule #20: COX7c
+Macromolecule #21: ZINC ION
+Macromolecule #22: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #23: CARDIOLIPIN
+Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #25: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #26: HEME C
+Macromolecule #27: HEME-A
+Macromolecule #28: COPPER (II) ION
+Macromolecule #29: MAGNESIUM ION
+Macromolecule #30: DINUCLEAR COPPER ION
+Macromolecule #31: LYSINE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.8 Component:
| |||||||||||||||
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 |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |