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Open data
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Basic information
Entry | Database: PDB / ID: 8.0E+73 | ||||||
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Title | Vigna radiata supercomplex I+III2 (full bridge) | ||||||
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![]() | ELECTRON TRANSPORT / respiratory supercomplex / nadh-cyt c oxidoreductase / membrane complex | ||||||
Function / homology | ![]() TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / protein insertion into mitochondrial inner membrane / : / quinol-cytochrome-c reductase / oxidoreductase activity, acting on NAD(P)H / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) ...TIM22 mitochondrial import inner membrane insertion complex / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / protein insertion into mitochondrial inner membrane / : / quinol-cytochrome-c reductase / oxidoreductase activity, acting on NAD(P)H / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / catalytic activity / quinone binding / ATP synthesis coupled electron transport / respiratory electron transport chain / mitochondrial membrane / electron transport chain / mitochondrial intermembrane space / metalloendopeptidase activity / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / heme binding / mitochondrion / proteolysis / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Maldonado, M. / Letts, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Plant-specific features of respiratory supercomplex I + III from Vigna radiata. Authors: M Maldonado / Z Fan / K M Abe / J A Letts / ![]() Abstract: The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane ...The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 294.1 KB | Display | |
Data in CIF | ![]() | 468.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27934MC 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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1 |
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Components
+Protein , 57 types, 66 molecules AMCODPEQFRGSHTJVKW1M2M3M4M4L5M6MA1A2A3A5A6...
-MPP-alpha (protomer ... , 2 types, 2 molecules BN
#2: Protein | Mass: 55244.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#11: Protein | Mass: 54537.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 13 types, 46 molecules ![](data/chem/img/PC1.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
#60: Chemical | ChemComp-PC1 / #61: Chemical | ChemComp-CDL / #62: Chemical | ChemComp-HEM / #63: Chemical | ChemComp-3PE / #64: Chemical | #65: Chemical | ChemComp-U10 / | #66: Chemical | ChemComp-NDP / | #67: Chemical | #68: Chemical | ChemComp-FE / | #69: Chemical | #70: Chemical | ChemComp-SF4 / #71: Chemical | #72: Chemical | ChemComp-FMN / | |
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-Details
Has ligand of interest | N |
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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: Vigna radiata supercomplex I+III2 (full bridge) / Type: COMPLEX Details: Higher-order assembly between respiratory complex I and complex III2 Entity ID: #1-#59 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.7 Details: 0.2% digitonin, 30 mM HEPES pH 7.7, 150 mM potassium acetate, 1 mM EDTA, 0.002% PMSF |
Specimen | Conc.: 1.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Digitonin-extracted, amphipol (A8-35)stabilized |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Details: 4 ul, 20 seconds pre-blot, blot 4 seconds |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 25712 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123451 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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