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Open data
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Basic information
Entry | Database: PDB / ID: 6qc6 | ||||||
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Title | Ovine respiratory complex I FRC open class 1 | ||||||
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![]() | ELECTRON TRANSPORT / complex I / cellular respiration / mitochondria | ||||||
Function / homology | ![]() NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity ...NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Letts, J.A. / Sazanov, L.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk. Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov / ![]() ![]() ![]() Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4498MC ![]() 4479C ![]() 4480C ![]() 4481C ![]() 4482C ![]() 4493C ![]() 4494C ![]() 4495C ![]() 4496C ![]() 4497C ![]() 4499C ![]() 4500C ![]() 4501C ![]() 4502C ![]() 4505C ![]() 4506C ![]() 4507C ![]() 6q9bC ![]() 6q9dC ![]() 6q9eC ![]() 6qa9C ![]() 6qbxC ![]() 6qc2C ![]() 6qc3C ![]() 6qc4C ![]() 6qc5C ![]() 6qc7C ![]() 6qc8C ![]() 6qc9C ![]() 6qcaC ![]() 6qcfC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2
#1: Protein | Mass: 48678.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 23840.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase core subunit ... , 3 types, 3 molecules S1S3S7
#3: Protein | Mass: 77031.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 26441.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 3 types, 3 molecules S2S8S6
#4: Protein | Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#7: Protein | Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase subunit ... , 13 types, 13 molecules V3S4A9A6A7B5BJS5A3B3B4B9B2
#8: Protein | Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 15375.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 38660.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 14923.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 12399.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 16714.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 12474.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#31: Protein | Mass: 9194.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#32: Protein | Mass: 11015.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 14975.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 21648.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 8500.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 7 types, 7 molecules A2A5ALAKA8AJAM
#12: Protein | Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#13: Protein | Mass: 13156.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 14610.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 20008.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 36803.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 3 molecules AAABA1
#17: Protein | Mass: 10119.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #44: Protein | | Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules D3D1D64LD5D4D2
#18: Protein | Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating) |
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#19: Protein | Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating) |
#20: Protein | Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating) |
#21: Protein | Mass: 10840.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating) |
#22: Protein | Mass: 68410.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating) |
#23: Protein | Mass: 52058.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating) |
#24: Protein | Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules C2C1
#33: Protein | Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#42: Protein/peptide | Mass: 5808.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 5 types, 5 molecules B6B7B8BKB1
#36: Protein | Mass: 15433.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#37: Protein | Mass: 16282.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 18818.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 14455.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 6930.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 9 types, 18 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PC1.gif)
#45: Chemical | ChemComp-SF4 / #46: Chemical | ChemComp-FMN / | #47: Chemical | #48: Chemical | ChemComp-ZN / | #49: Chemical | ChemComp-NDP / | #50: Chemical | #51: Chemical | #52: Chemical | ChemComp-CDL / | #53: Chemical | ChemComp-PC1 / | |
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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: Ovine mitochondrial respiratory complex I / Type: COMPLEX Details: Open class 1 from ovine mitochondrial respiratory complex I Entity ID: #1-#44 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.4 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 95 % / Chamber temperature: 277 K Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing |
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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 / Calibrated magnification: 100000 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1854 |
Image scans | Movie frames/image: 34 |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 400000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26978 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 75 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5LNK |