+Open data
-Basic information
Entry | Database: PDB / ID: 6zk9 | |||||||||
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Title | Peripheral domain of open complex I during turnover | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein | |||||||||
Function / homology | Function and homology information NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / acyl carrier activity / : / ATP metabolic process / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process ...NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / acyl carrier activity / : / ATP metabolic process / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / circadian rhythm / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Kampjut, D. / Sazanov, L.A. | |||||||||
Funding support | European Union, 2items
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Citation | Journal: Science / Year: 2020 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zk9.cif.gz | 775.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zk9.ent.gz | 619.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/6zk9 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/6zk9 | HTTPS FTP |
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-Related structure data
Related structure data | 11241MC 6zkaC 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NADH dehydrogenase [ubiquinone] ... , 4 types, 4 molecules 1cei
#1: Protein | Mass: 50687.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating) |
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#10: Protein | Mass: 19381.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PE07 |
#12: Protein | Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QAH8 |
#16: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: B9VGZ9 |
-Mitochondrial complex I, ... , 9 types, 9 molecules 2469abfhq
#2: Protein | Mass: 27373.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NRY1 |
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#4: Protein | Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#6: Protein | Mass: 24622.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#7: Protein | Mass: 24496.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#8: Protein | Mass: 11916.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#9: Protein | Mass: 13457.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#13: Protein | Mass: 13287.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PNX7 |
#15: Protein | Mass: 12701.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P0I2 |
#18: Protein | Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
-NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules 35
#3: Protein | Mass: 79519.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB34 |
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#5: Protein | Mass: 30384.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PB27 |
-NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules dg
#11: Protein | Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PI58 |
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#14: Protein | Mass: 16302.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QC06 |
-Protein , 1 types, 1 molecules j
#17: Protein | Mass: 17608.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7 |
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-Non-polymers , 12 types, 1491 molecules
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | ChemComp-NAI / | #22: Chemical | #23: Chemical | ChemComp-K / | #24: Chemical | #25: Chemical | #26: Chemical | ChemComp-ZN / | #27: Chemical | ChemComp-NDP / | #28: Chemical | ChemComp-ZMP / | #29: Chemical | ChemComp-CDL / | #30: 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 |
-Sample preparation
Component | Name: Peripheral domain of open complex I during turnover / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: Ovis aries (sheep) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315484 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 38 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5LNK | ||||||||||||||||||||||||||||
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