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Yorodumi- PDB-8bpx: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bpx | ||||||
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Plant / Mitochondria / Complex | ||||||
Function / homology | Function and homology information plastid outer membrane / anther dehiscence / TIM22 mitochondrial import inner membrane insertion complex / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / P450-containing electron transport chain ...plastid outer membrane / anther dehiscence / TIM22 mitochondrial import inner membrane insertion complex / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / respiratory chain complex III / mitochondrial processing peptidase / plant-type cell wall / cold acclimation / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / protein insertion into mitochondrial inner membrane / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / : / quinol-cytochrome-c reductase / plant-type vacuole / vacuole / respiratory chain complex I / regulation of reactive oxygen species metabolic process / ubiquinol-cytochrome-c reductase activity / response to osmotic stress / NADH dehydrogenase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / porin activity / cobalt ion binding / pore complex / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / monoatomic ion transport / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to salt stress / respiratory electron transport chain / chloroplast / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / carbonate dehydratase activity / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / transmembrane transport / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / peroxisome / 4 iron, 4 sulfur cluster binding / mitochondrial outer membrane / carbohydrate metabolic process / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / heme 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.09 Å | ||||||
Authors | Klusch, N. / Kuehlbrandt, W. | ||||||
Funding support | Germany, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bpx.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8bpx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpx ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpx | HTTPS FTP |
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-Related structure data
Related structure data | 16168MC 8bedC 8beeC 8befC 8behC 8belC 8bepC 8bq5C 8bq6C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 8 types, 8 molecules BCDGIQRe
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules EF
+Protein , 12 types, 14 molecules OYbcdfgimxACBCAEBE
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules PSWXZa
+Acyl carrier protein ... , 2 types, 2 molecules TU
+Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop
+Uncharacterized protein ... , 2 types, 2 molecules uv
+Gamma carbonic anhydrase ... , 2 types, 2 molecules yz
+Probable mitochondrial-processing peptidase subunit ... , 2 types, 4 molecules AABAABBB
+Cytochrome b-c1 complex subunit ... , 6 types, 12 molecules ADBDAFBFAGBGAHBHAIBIAJBJ
+Non-polymers , 19 types, 4925 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete composition) Type: COMPLEX / Entity ID: #1-#57 / Source: NATURAL |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1215138 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||
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