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Yorodumi- EMDB-16007: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16007 | |||||||||
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information respiratory chain complex III / mitochondrial respiratory chain complex III / vacuole / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding ...respiratory chain complex III / mitochondrial respiratory chain complex III / vacuole / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / thale cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.25 Å | |||||||||
Authors | Klusch N / Kuehlbrandt W | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Plants / Year: 2023 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16007.map.gz | 64.1 MB | EMDB map data format | |
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Header (meta data) | emd-16007-v30.xml emd-16007.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16007_fsc.xml | 26.5 KB | Display | FSC data file |
Images | emd_16007.png | 173.4 KB | ||
Others | emd_16007_additional_1.map.gz emd_16007_half_map_1.map.gz emd_16007_half_map_2.map.gz | 91.1 MB 1 GB 1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16007 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16007 | HTTPS FTP |
-Related structure data
Related structure data | 8belMC 8bedC 8beeC 8befC 8behC 8bepC 8bpxC 8bq5C 8bq6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16007.map.gz / Format: CCP4 / Size: 68.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Additional map: #1
File | emd_16007_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16007_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16007_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII memb...
+Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII memb...
+Macromolecule #1: Cytochrome b
+Macromolecule #2: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
+Macromolecule #3: Cytochrome c1 2, heme protein, mitochondrial
+Macromolecule #4: Cytochrome b-c1 complex subunit 8-1, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit 6-1, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #7: Cytochrome b-c1 complex subunit 10, mitochondrial
+Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #9: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14...
+Macromolecule #10: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
+Macromolecule #11: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #12: CARDIOLIPIN
+Macromolecule #13: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #15: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #16: UBIQUINONE-7
+Macromolecule #17: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...
+Macromolecule #18: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000 |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Software | Name: Coot (ver. 0.9.5) |
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Refinement | Space: REAL |
Output model | PDB-8bel: |