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- PDB-8bee: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
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Basic information
Entry | Database: PDB / ID: 8bee | ||||||
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core) | ||||||
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![]() | MEMBRANE PROTEIN / Plant / Mitochondria / Complex | ||||||
Function / homology | ![]() photorespiration / embryo development ending in seed dormancy / respiratory chain complex I / ubiquinone-6 biosynthetic process / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / chloroplast thylakoid membrane ...photorespiration / embryo development ending in seed dormancy / respiratory chain complex I / ubiquinone-6 biosynthetic process / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / chloroplast thylakoid membrane / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / transmembrane transport / NAD binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial matrix / protein-containing complex binding / mitochondrion / zinc ion binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 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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PDBx/mmCIF format | ![]() | 357.5 KB | Display | ![]() |
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PDB format | ![]() | 274.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 70.2 KB | Display | |
Data in CIF | ![]() | 108.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15999MC ![]() 8bedC ![]() 8befC ![]() 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 dehydrogenase [ubiquinone] iron-sulfur protein ... , 3 types, 3 molecules BCI
#1: Protein | Mass: 24071.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q42577, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 22910.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q95748, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 25536.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q42599, NADH:ubiquinone reductase (H+-translocating) |
-Protein , 2 types, 2 molecules DU
#3: Protein | Mass: 45036.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 14183.111 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 PWZ
#5: Protein | Mass: 43988.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#8: Protein | Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq
#7: Protein | Mass: 19201.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 18346.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 636 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | #12: Chemical | ChemComp-NDP / | #13: Chemical | ChemComp-8Q1 / | #14: 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 peripheral core) Type: COMPLEX / Entity ID: #1-#10 / 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: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||
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