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Open data
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Basic information
Entry | Database: PDB / ID: 6zka | |||||||||
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Title | Membrane domain of open complex I during turnover | |||||||||
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![]() | ELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein | |||||||||
Function / homology | ![]() NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / reactive oxygen species metabolic process / : ...NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / reactive oxygen species metabolic process / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial intermembrane space / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
![]() | Kampjut, D. / Sazanov, L.A. | |||||||||
Funding support | European Union, 2items
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![]() | ![]() Title: The coupling mechanism of mammalian respiratory complex I. Authors: Domen Kampjut / Leonid A Sazanov / ![]() Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. | |||||||||
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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 MB | Display | ![]() |
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PDB format | ![]() | 853.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11242MC ![]() 6zk9C ![]() 6zkbC ![]() 6zkcC ![]() 6zkdC ![]() 6zkeC ![]() 6zkfC ![]() 6zkgC ![]() 6zkhC ![]() 6zkiC ![]() 6zkjC ![]() 6zkkC ![]() 6zklC ![]() 6zkmC ![]() 6zknC ![]() 6zkoC ![]() 6zkpC ![]() 6zkqC ![]() 6zkrC ![]() 6zksC ![]() 6zktC ![]() 6zkuC ![]() 6zkvC M: map data used to model this data C: citing same article ( |
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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-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#1: 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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#2: 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) |
#3: 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) |
#4: Protein | Mass: 10868.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 68438.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 52086.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating) |
#7: 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) |
-Mitochondrial complex I, ... , 9 types, 9 molecules VZqrwxyz4
#8: Protein | Mass: 14784.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 15565.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 17410.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 8802.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 7075.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 52634.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase subunit ... , 8 types, 8 molecules Wlmnpstu
#9: Protein | Mass: 21614.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#14: Protein | Mass: 12605.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 9325.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 11146.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 15236.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 16413.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 21779.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 12226.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules X
#10: Protein | Mass: 17608.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-NADH dehydrogenase [ubiquinone] 1 ... , 4 types, 4 molecules Ykov
#11: Protein | Mass: 20139.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#13: Protein | Mass: 40557.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 14431.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 21752.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 8 types, 1321 molecules ![](data/chem/img/PC1.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
#30: Chemical | ChemComp-PC1 / #31: Chemical | ChemComp-DCQ / | #32: Chemical | ChemComp-3PE / #33: Chemical | ChemComp-CDL / #34: Chemical | ChemComp-ZMP / | #35: Chemical | ChemComp-AMP / | #36: Chemical | ChemComp-MYR / | #37: Water | ChemComp-HOH / | |
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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: Membrane domain of open complex I during turnover / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 / Cs: 2.7 mm |
Image recording | Electron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315484 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5LNK | ||||||||||||||||||||||||||||
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