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- PDB-8bef: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
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Basic information
Entry | Database: PDB / ID: 8bef | ||||||
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core) | ||||||
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![]() | MEMBRANE PROTEIN / Plant / Mitochondria / Complex | ||||||
Function / homology | ![]() plastid outer membrane / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / mitochondrion targeting sequence binding / TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration ...plastid outer membrane / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / mitochondrion targeting sequence binding / 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 / respiratory chain complex I / regulation of reactive oxygen species metabolic process / plastid / porin activity / pore complex / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / : / mitochondrial electron transport, NADH to ubiquinone / respirasome / protein transmembrane transporter activity / mitochondrial respiratory chain complex I assembly / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / electron transport coupled proton transport / monoatomic ion transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / mitochondrial outer membrane / mitochondrial inner membrane / copper ion binding / nucleolus / protein homodimerization activity / mitochondrion / extracellular region / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.13 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 699 KB | Display | ![]() |
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PDB format | ![]() | 557.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 127.5 KB | Display | |
Data in CIF | ![]() | 185.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 16000MC ![]() 8bedC ![]() 8beeC ![]() 8behC ![]() 8belC ![]() 8bepC ![]() 8bpxC ![]() 8bq5C ![]() 8bq6C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#1: Protein | Mass: 13969.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P92533, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 36020.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: B5TM92, NADH:ubiquinone reductase (H+-translocating) |
#3: Protein | Mass: 23690.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A2P2CLG1, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 11193.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q04614, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 74497.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: B5TM94, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 55995.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P93313, NADH:ubiquinone reductase (H+-translocating) |
#7: Protein | Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O05000, NADH:ubiquinone reductase (H+-translocating) |
-Protein , 8 types, 8 molecules OYbdefix
#8: Protein | Mass: 17626.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 17017.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 11383.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 27985.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 3 types, 3 molecules XZa
#9: Protein | Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#11: Protein | Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Uncharacterized protein ... , 2 types, 2 molecules uv
#18: Protein | Mass: 7546.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#19: Protein | Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Gamma carbonic anhydrase ... , 2 types, 2 molecules yz
#21: Protein | Mass: 30102.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9C6B3, Lyases; Carbon-oxygen lyases; Hydro-lyases |
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#22: Protein | Mass: 30010.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases |
-Non-polymers , 12 types, 1315 molecules ![](data/chem/img/PGT.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/UQ5.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/BCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/Q7G.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/UQ5.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/BCO.gif)
![](data/chem/img/HOH.gif)
#23: Chemical | ChemComp-PGT / ( #24: Chemical | ChemComp-UQ9 / | #25: Chemical | ChemComp-PTY / #26: Chemical | ChemComp-Q7G / #27: Chemical | ChemComp-FE / | #28: Chemical | ChemComp-UQ5 / | #29: Chemical | #30: Chemical | #31: Chemical | #32: Chemical | ChemComp-ZN / | #33: Chemical | ChemComp-BCO / | #34: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane core) Type: COMPLEX / Entity ID: #1-#22 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
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 |
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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: ![]() |
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) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||
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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: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.89 Å2 | ||||||||||||||||||||||||||||
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