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- PDB-7zkp: Late assembly intermediate of the proximal proton pumping module ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zkp | ||||||
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Title | Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84 | ||||||
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![]() | ELECTRON TRANSPORT / assembly respiratory chain membrane protein mitochondria | ||||||
Function / homology | ![]() NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / aerobic respiration / mitochondrial membrane / mitochondrial intermembrane space ...NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / aerobic respiration / mitochondrial membrane / mitochondrial intermembrane space / oxidoreductase activity / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Schiller, J. / Laube, E. / Vonck, J. / Zickermann, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling. Authors: Jonathan Schiller / Eike Laube / Ilka Wittig / Werner Kühlbrandt / Janet Vonck / Volker Zickermann / ![]() Abstract: Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly ...Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 456.6 KB | Display | ![]() |
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PDB format | ![]() | 365.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.9 KB | Display | ![]() |
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Full document | ![]() | 882.8 KB | Display | |
Data in XML | ![]() | 54.2 KB | Display | |
Data in CIF | ![]() | 78.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14764MC ![]() 7zkqC 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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Components
-Protein , 10 types, 10 molecules DUWX2gb9CA
#1: Protein | Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 53381.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: S5U4R9, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 8992.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 8059.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 97098.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 32629.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NDUFAF1 has a C-terminal strep tag / Source: (gene. exp.) ![]() ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 4 types, 4 molecules L136
#2: Protein | Mass: 9843.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: S5U4U1, NADH:ubiquinone reductase (H+-translocating) |
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#6: Protein | Mass: 38389.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: S5U3V2, NADH:ubiquinone reductase (H+-translocating) |
#8: Protein | Mass: 14506.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: S5TMS4, NADH:ubiquinone reductase (H+-translocating) |
#9: Protein | Mass: 20793.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: S5U3X7, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/CDL.gif)
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#15: Chemical | #16: Chemical | ChemComp-PLC / | #17: Chemical | ChemComp-CPL / | #18: Chemical | ChemComp-3PE / | #19: Chemical | ChemComp-T7X / | |
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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: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84 Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was a mixture of assembly intermediates associated with the assembly factor NDUFAF1 |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6229 |
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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: 2048808 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18279 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7O71 |