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- EMDB-16168: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
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Open data
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Basic information
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition) | |||||||||
![]() | Composite density-modified map | |||||||||
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Function / homology | ![]() plastid outer membrane / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain ...plastid outer membrane / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / protein insertion into mitochondrial inner membrane / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / respiratory chain complex I / vacuole / ubiquinol-cytochrome-c reductase activity / regulation of reactive oxygen species metabolic process / ubiquinone-6 biosynthetic process / response to osmotic stress / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / porin activity / pore complex / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / respirasome / chloroplast thylakoid membrane / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / monoatomic ion transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrial membrane / electron transport chain / carbonate dehydratase activity / mitochondrial intermembrane space / transmembrane transport / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / peroxisome / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial outer membrane / response to oxidative stress / mitochondrial inner membrane / carbohydrate metabolic process / oxidoreductase activity / electron transfer activity / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex binding / nucleolus / protein homodimerization activity / mitochondrion / proteolysis / zinc ion binding / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.09 Å | |||||||||
![]() | Klusch N / Kuehlbrandt W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution. Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun / ![]() Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 198.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 75.8 KB 75.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.8 KB | Display | ![]() |
Images | ![]() | 177.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 396 KB | Display | ![]() |
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Full document | ![]() | 395.5 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bpxMC ![]() 8bedC ![]() 8beeC ![]() 8befC ![]() 8behC ![]() 8belC ![]() 8bepC ![]() 8bq5C ![]() 8bq6C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | Composite density-modified map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.573 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete ...
+Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete ...
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: 2Fe-2S ferredoxin-like superfamily protein
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein 1, mitochondrial
+Macromolecule #21: Acyl carrier protein 2, mitochondrial
+Macromolecule #22: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
+Macromolecule #25: Outer envelope pore protein 16-3, chloroplastic/mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #28: At2g46540/F11C10.23
+Macromolecule #29: Transmembrane protein
+Macromolecule #30: Excitatory amino acid transporter
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
+Macromolecule #32: At4g16450
+Macromolecule #33: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
+Macromolecule #34: At1g67350
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: AT2G31490 protein
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
+Macromolecule #42: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: Uncharacterized protein At1g67785
+Macromolecule #44: Uncharacterized protein At2g27730, mitochondrial
+Macromolecule #45: Gamma carbonic anhydrase-like 2, mitochondrial
+Macromolecule #46: Gamma carbonic anhydrase 2, mitochondrial
+Macromolecule #47: Gamma carbonic anhydrase 1, mitochondrial
+Macromolecule #48: Probable mitochondrial-processing peptidase subunit alpha-1, mito...
+Macromolecule #49: Probable mitochondrial-processing peptidase subunit beta, mitocho...
+Macromolecule #50: Cytochrome b
+Macromolecule #51: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
+Macromolecule #52: Cytochrome c1 2, heme protein, mitochondrial
+Macromolecule #53: Cytochrome b-c1 complex subunit 7-2, mitochondrial
+Macromolecule #54: Cytochrome b-c1 complex subunit 8-1, mitochondrial
+Macromolecule #55: Cytochrome b-c1 complex subunit 6-1, mitochondrial
+Macromolecule #56: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #57: Cytochrome b-c1 complex subunit 10, mitochondrial
+Macromolecule #58: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #59: IRON/SULFUR CLUSTER
+Macromolecule #60: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #61: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #62: FLAVIN MONONUCLEOTIDE
+Macromolecule #63: Ubiquinone-9
+Macromolecule #64: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...
+Macromolecule #65: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #66: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #67: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14...
+Macromolecule #68: FE (III) ION
+Macromolecule #69: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #70: ZINC ION
+Macromolecule #71: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #72: CARDIOLIPIN
+Macromolecule #73: CROTONYL COENZYME A
+Macromolecule #74: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #75: UBIQUINONE-7
+Macromolecule #76: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.18 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Software | Name: ![]() |
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Refinement | Space: REAL |
Output model | ![]() PDB-8bpx: |