+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27934 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Vigna radiata supercomplex I+III2 (full bridge) | |||||||||
Map data | Vigna radiata supercomplex I III2 (SC I III2) composite map of full supercomplex (bridged class 1). | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / protein insertion into mitochondrial inner membrane / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) ...TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / protein insertion into mitochondrial inner membrane / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / quinone binding / catalytic activity / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / RNA binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Vigna radiata (mung bean) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Maldonado M / Letts JA | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nat Plants / Year: 2023 Title: Plant-specific features of respiratory supercomplex I + III from Vigna radiata. Authors: M Maldonado / Z Fan / K M Abe / J A Letts / Abstract: The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane ...The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27934.map.gz | 81.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27934-v30.xml emd-27934.xml | 79 KB 79 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27934_fsc.xml emd_27934_fsc_2.xml emd_27934_fsc_3.xml emd_27934_fsc_4.xml emd_27934_fsc_5.xml emd_27934_fsc_6.xml emd_27934_fsc_7.xml emd_27934_fsc_8.xml | 19.9 KB 19.9 KB 19.9 KB 19.9 KB 19.9 KB 19.9 KB 20 KB 19.9 KB | Display Display Display Display Display Display Display Display | FSC data file |
Images | emd_27934.png | 86.8 KB | ||
Masks | emd_27934_msk_1.map | 824 MB | Mask map | |
Others | emd_27934_additional_1.map.gz emd_27934_half_map_1.map.gz emd_27934_half_map_2.map.gz | 779.1 MB 764 MB 764 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27934 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27934 | HTTPS FTP |
-Validation report
Summary document | emd_27934_validation.pdf.gz | 946.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27934_full_validation.pdf.gz | 946.2 KB | Display | |
Data in XML | emd_27934_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_27934_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27934 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27934 | HTTPS FTP |
-Related structure data
Related structure data | 8e73MC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27934.map.gz / Format: CCP4 / Size: 87.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Vigna radiata supercomplex I III2 (SC I III2) composite map of full supercomplex (bridged class 1). | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_27934_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Vigna radiata supercomplex I III2 bridged class 1
File | emd_27934_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Vigna radiata supercomplex I III2 bridged class 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Vigna radiata supercomplex I III2 bridged class 1 half map B
File | emd_27934_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Vigna radiata supercomplex I III2 bridged class 1_half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Vigna radiata supercomplex I III2 bridged class 1 half map A
File | emd_27934_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Vigna radiata supercomplex I III2 bridged class 1_half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Vigna radiata supercomplex I+III2 (full bridge)
+Supramolecule #1: Vigna radiata supercomplex I+III2 (full bridge)
+Macromolecule #1: MPP-beta
+Macromolecule #2: MPP-alpha (protomer 1)
+Macromolecule #3: COB (cyt b)
+Macromolecule #4: CYC1 (cyt c1)
+Macromolecule #5: UCR1 (Rieske iron-sulfur protein subunit)
+Macromolecule #6: QCR7
+Macromolecule #7: QCR8
+Macromolecule #8: QCR6
+Macromolecule #9: QCR9
+Macromolecule #10: QCR10 (UCRY)
+Macromolecule #11: MPP-alpha (protomer 2)
+Macromolecule #12: Nad1
+Macromolecule #13: Nad2
+Macromolecule #14: Nad3
+Macromolecule #15: Nad4
+Macromolecule #16: Nad4L
+Macromolecule #17: Nad5
+Macromolecule #18: Nad6
+Macromolecule #19: NDUA1
+Macromolecule #20: NDUA2
+Macromolecule #21: NDUA3
+Macromolecule #22: NDUA5
+Macromolecule #23: NDUA6
+Macromolecule #24: NDUA7
+Macromolecule #25: NDUA8
+Macromolecule #26: NDUA9
+Macromolecule #27: NDUA11
+Macromolecule #28: NDUA12
+Macromolecule #29: NDUA13
+Macromolecule #30: NDUAB1-beta
+Macromolecule #31: NDUAB1-alpha
+Macromolecule #32: NDUB2
+Macromolecule #33: NDUB3
+Macromolecule #34: NDUB4
+Macromolecule #35: NDUB7
+Macromolecule #36: NDUB8
+Macromolecule #37: NDUB9
+Macromolecule #38: NDUB10
+Macromolecule #39: NDUB11
+Macromolecule #40: NDUFX
+Macromolecule #41: NDUC2
+Macromolecule #42: NDUP2
+Macromolecule #43: NDUCA1
+Macromolecule #44: NDUCA2
+Macromolecule #45: NDUCAL2
+Macromolecule #46: NDUS1
+Macromolecule #47: NDUS2
+Macromolecule #48: NDUS3
+Macromolecule #49: NDUS4
+Macromolecule #50: NDUS5
+Macromolecule #51: NDUS6
+Macromolecule #52: NDUS7
+Macromolecule #53: NDUS8
+Macromolecule #54: NDUP1
+Macromolecule #55: NDUP4
+Macromolecule #56: NDUB6
+Macromolecule #57: NDUV1
+Macromolecule #58: NDUV2
+Macromolecule #59: NDUX1
+Macromolecule #60: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #61: CARDIOLIPIN
+Macromolecule #62: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #63: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #64: HEME C
+Macromolecule #65: UBIQUINONE-10
+Macromolecule #66: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #67: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #68: FE (III) ION
+Macromolecule #69: ZINC ION
+Macromolecule #70: IRON/SULFUR CLUSTER
+Macromolecule #71: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #72: FLAVIN MONONUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.55 mg/mL |
---|---|
Buffer | pH: 7.7 Details: 0.2% digitonin, 30 mM HEPES pH 7.7, 150 mM potassium acetate, 1 mM EDTA, 0.002% PMSF |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP / Details: 4 ul, 20 seconds pre-blot, blot 4 seconds. |
Details | Digitonin-extracted, amphipol (A8-35)stabilized |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 25712 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-8e73: |