+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22090 | |||||||||
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Title | Vigna radiata mitochondrial complex I* | |||||||||
Map data | Composite map of Vigna radiata mitochondrial complex I* from the combination of locally refined maps of the membrane arm and peripheral arm. Composite map was generated using PHENIX. | |||||||||
Sample |
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Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / catalytic activity ...oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / catalytic activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 / oxidoreductase activity / mitochondrion / RNA binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Vigna radiata (mung bean) / mung bean (mung bean) / Mung bean (mung bean) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Letts JA / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22090.map.gz | 479.9 MB | EMDB map data format | |
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Header (meta data) | emd-22090-v30.xml emd-22090.xml | 47 KB 47 KB | Display Display | EMDB header |
Images | emd_22090.png | 64.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22090 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22090 | HTTPS FTP |
-Related structure data
Related structure data | 6x89MC M: atomic model generated by this map 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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22090.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of Vigna radiata mitochondrial complex I* from the combination of locally refined maps of the membrane arm and peripheral arm. Composite map was generated using PHENIX. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Vigna radiata complex I*
+Supramolecule #1: Vigna radiata complex I*
+Macromolecule #1: Unknown Peptide
+Macromolecule #2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #3: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mit...
+Macromolecule #4: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #5: NDUA7
+Macromolecule #6: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
+Macromolecule #9: NDUS2
+Macromolecule #10: NDUS3
+Macromolecule #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #15: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #16: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #17: NU1M
+Macromolecule #18: NU2M
+Macromolecule #19: NU3M
+Macromolecule #20: NU4L
+Macromolecule #21: NU6M
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #23: uncharacterized protein LOC106754061
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
+Macromolecule #26: Unknown Peptide
+Macromolecule #27: Unknown Peptide
+Macromolecule #28: NDUC2
+Macromolecule #29: Protein At2g27730, mitochondrial
+Macromolecule #30: serine/arginine-rich-splicing factor SR34 isoform X2
+Macromolecule #31: NDUX1
+Macromolecule #32: gamma carbonic anhydrase 1, mitochondrial
+Macromolecule #33: gamma carbonic anhydrase 1, mitochondrial-like
+Macromolecule #34: gamma carbonic anhydrase-like 2, mitochondrial
+Macromolecule #35: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #36: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #37: IRON/SULFUR CLUSTER
+Macromolecule #38: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #39: ZINC ION
+Macromolecule #40: FLAVIN MONONUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: 30 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III Details: Blotted for 9 seconds at 100% humidity, 15 degrees C.. | |||||||||||||||
Details | Extracted from V. radiata mitochondrial membranes with digitonin, exchanged into amphipole A8-35, purified on sucrose gradient. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 190951 |
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CTF correction | Software - Name: CTFFIND |
Startup model | Type of model: INSILICO MODEL / In silico model: Ab initio |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Number classes: 3 / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 34407 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6x89: |