+Open data
-Basic information
Entry | Database: PDB / ID: 6x89 | ||||||
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Title | Vigna radiata mitochondrial complex I* | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / respiration / mitochondria / electron transport chain / complex I | ||||||
Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrion / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Vigna radiata (mung bean) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Letts, J.A. / Maldonado, M. / Padavannil, A. / Zhou, L. / Guo, F. | ||||||
Citation | Journal: Elife / Year: 2020 Title: Atomic structure of a mitochondrial complex I intermediate from vascular plants. Authors: Maria Maldonado / Abhilash Padavannil / Long Zhou / Fei Guo / James A Letts / Abstract: Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large ...Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC. For plants, limited availability of mitochondrial material has curbed detailed biochemical and structural studies of their mETC. Here, we present the cryoEM structure of the known CI assembly intermediate CI* from at 3.9 Å resolution. CI* contains CI's NADH-binding and CoQ-binding modules, the proximal-pumping module and the plant-specific γ-carbonic-anhydrase domain (γCA). Our structure reveals significant differences in core and accessory subunits of the plant complex compared to yeast, mammals and bacteria, as well as the details of the γCA domain subunit composition and membrane anchoring. The structure sheds light on differences in CI assembly across lineages and suggests potential physiological roles for CI* beyond assembly. | ||||||
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 | 6x89.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6x89.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6x89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x89_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6x89_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6x89_validation.xml.gz | 160.7 KB | Display | |
Data in CIF | 6x89_validation.cif.gz | 243.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/6x89 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/6x89 | HTTPS FTP |
-Related structure data
Related structure data | 22090MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10586 (Title: Cryo electron micrographs of digitonin-solubilized, amphipol-stabilized, sucrose-gradient-purified V. radiata mitochondrial membranes - mixed fraction containing CI*, CIII2 and SC III2+IV Data size: 6.7 TB Data #1: Raw movies of mixed sample used for determination of mung bean respiratory CI*, CIII2, CIV and SC III2+IV [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein/peptide , 3 types, 3 molecules ABC
#1: Protein/peptide | Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
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#26: Protein/peptide | Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#27: Protein/peptide | Mass: 3677.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 8 types, 8 molecules A2A5A6A9ALA1A8AM
#2: Protein | Mass: 10884.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TVC7 |
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#3: Protein | Mass: 18977.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3U023 |
#4: Protein | Mass: 14920.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3W1K8 |
#6: Protein | Mass: 43781.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3V8W7 |
#7: Protein | Mass: 18192.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VNK7 |
#22: Protein | Mass: 7357.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TU57 |
#24: Protein | Mass: 12022.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VVN6 |
#25: Protein | Mass: 16189.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UYW0 |
-Protein , 14 types, 14 molecules A7S2S31M2M3M4L6MA3C2P2S5X1L2
#5: Protein | Mass: 14356.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UVC7 |
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#9: Protein | Mass: 44813.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#10: Protein | Mass: 22806.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#17: Protein | Mass: 35651.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#18: Protein | Mass: 53900.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#19: Protein | Mass: 13507.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#20: Protein | Mass: 11082.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#21: Protein | Mass: 23484.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
#23: Protein | Mass: 6695.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TCK0 |
#28: Protein | Mass: 9130.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UPL8 |
#29: Protein | Mass: 12172.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TGE7 |
#30: Protein | Mass: 45640.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ33 |
#31: Protein | Mass: 10949.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VI15 |
#34: Protein | Mass: 28268.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UI49 |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules S1S4S6S7S8
#8: Protein | Mass: 81434.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ85 |
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#11: Protein | Mass: 16435.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UIW7 |
#12: Protein | Mass: 11582.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VYF3 |
#13: Protein | Mass: 23710.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3U8J5 |
#14: Protein | Mass: 25545.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VGS8 |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2
#15: Protein | Mass: 53817.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata References: UniProt: A0A1S3V7V2, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating) |
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#16: Protein | Mass: 27992.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U769 |
-Gamma carbonic anhydrase 1, ... , 2 types, 2 molecules G1G2
#32: Protein | Mass: 29333.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VT00 |
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#33: Protein | Mass: 29780.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3U544 |
-Non-polymers , 6 types, 18 molecules
#35: Chemical | ChemComp-NAP / | ||||||||
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#36: Chemical | ChemComp-PC1 / #37: Chemical | ChemComp-SF4 / #38: Chemical | #39: Chemical | #40: Chemical | ChemComp-FMN / | |
-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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: Vigna radiata complex I* / Type: COMPLEX Details: Complex I 800 kDa assembly intermediate (complex I*) Entity ID: #1-#34 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.8 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Vigna radiata (mung bean) | |||||||||||||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Extracted from V. radiata mitochondrial membranes with digitonin, exchanged into amphipole A8-35, purified on sucrose gradient. | |||||||||||||||||||||||||
Specimen support | Details: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE Details: Blotted for 9 seconds at 100% humidity, 15 degrees C. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 3 sec. / Electron dose: 86.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9816 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 190951 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34407 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||
Refine LS restraints |
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