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- PDB-6ziy: Respiratory complex I from Thermus thermophilus, NADH dataset, ma... -
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Basic information
Entry | Database: PDB / ID: 6ziy | ||||||
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Title | Respiratory complex I from Thermus thermophilus, NADH dataset, major state | ||||||
![]() | (NADH-quinone oxidoreductase subunit ...) x 15 | ||||||
![]() | MEMBRANE PROTEIN / Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation | ||||||
Function / homology | ![]() NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase activity / ubiquinone binding ...NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase activity / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å | ||||||
![]() | Kaszuba, K. / Tambalo, M. / Gallagher, G.T. / Sazanov, L.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Key role of quinone in the mechanism of respiratory complex I. Authors: Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov / ![]() ![]() ![]() Abstract: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 787.4 KB | Display | ![]() |
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PDB format | ![]() | 630.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 124.1 KB | Display | |
Data in CIF | ![]() | 194.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11231MC ![]() 6i0dC ![]() 6i1pC ![]() 6q8oC ![]() 6q8wC ![]() 6q8xC ![]() 6y11C ![]() 6zjlC ![]() 6zjnC ![]() 6zjyC 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-quinone oxidoreductase subunit ... , 15 types, 15 molecules 12345697AJKLMNH
#1: Protein | Mass: 48693.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56222, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#2: Protein | Mass: 20309.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56221, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#3: Protein | Mass: 86656.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56223, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#4: Protein | Mass: 46428.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56220, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#5: Protein | Mass: 23893.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56219, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#6: Protein | Mass: 20262.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56218, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#7: Protein | Mass: 20106.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56224, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#8: Protein | Mass: 14812.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q5SKZ7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#9: Protein | Mass: 13154.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56217, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#10: Protein | Mass: 18563.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56225, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#11: Protein | Mass: 10002.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56226, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#12: Protein | Mass: 65189.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56227, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#13: Protein | Mass: 49247.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56228, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#14: Protein | Mass: 44463.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56229, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#15: Protein | Mass: 41034.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q60019, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-Non-polymers , 4 types, 11 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
#16: Chemical | ChemComp-SF4 / #17: Chemical | ChemComp-FMN / | #18: Chemical | ChemComp-NAI / | #19: Chemical | |
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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: Respiratory complex I from Thermus thermophilus / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
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Molecular weight | Value: 0.53 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: with 5 mM NADH |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 defocus max: 4000 nm / Nominal defocus min: 2500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 2184 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 34 / Used frames/image: 1-34 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 205000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44500 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6Y11 |