[English] 日本語
Yorodumi- EMDB-4384: Cryo-EM structure of respiratory complex I from Yarrowia lipolytica -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4384 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of respiratory complex I from Yarrowia lipolytica | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / protein-containing complex binding / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Yarrowia lipolytica (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.32 Å | |||||||||
Authors | Parey K / Vonck J | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Elife / Year: 2018 Title: Cryo-EM structure of respiratory complex I at work. Authors: Kristian Parey / Ulrich Brandt / Hao Xie / Deryck J Mills / Karin Siegmund / Janet Vonck / Werner Kühlbrandt / Volker Zickermann / Abstract: Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 ...Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4384.map.gz | 334.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4384-v30.xml emd-4384.xml | 58.9 KB 58.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4384_fsc.xml | 16.3 KB | Display | FSC data file |
Images | emd_4384.png | 173.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4384 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4384 | HTTPS FTP |
-Validation report
Summary document | emd_4384_validation.pdf.gz | 317.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4384_full_validation.pdf.gz | 316.7 KB | Display | |
Data in XML | emd_4384_validation.xml.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4384 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4384 | HTTPS FTP |
-Related structure data
Related structure data | 6gcsMC 4385C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4384.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Mitochondrial NADH:ubiquinone oxidoreductase
+Supramolecule #1: Mitochondrial NADH:ubiquinone oxidoreductase
+Macromolecule #1: 75-KDA PROTEIN (NUAM)
+Macromolecule #2: 51-KDA PROTEIN (NUBM)
+Macromolecule #3: 49-KDA PROTEIN (NUCM)
+Macromolecule #4: NIMM SUBUNIT
+Macromolecule #5: NUEM SUBUNIT
+Macromolecule #6: NUFM SUBUNIT
+Macromolecule #7: 30-KDA PROTEIN (NUGM)
+Macromolecule #8: 24-KDA SUBUNIT (NUHM)
+Macromolecule #9: TYKY SUBUNIT (NUIM)
+Macromolecule #10: NUJM SUBUNIT
+Macromolecule #11: PSST SUBUNIT (NUKM)
+Macromolecule #12: ND4L SUBUNIT (NULM)
+Macromolecule #13: NUMM SUBUNIT
+Macromolecule #14: ACPM1 SUBUNIT
+Macromolecule #15: NB4M SUBUNIT
+Macromolecule #16: ACPM2 SUBUNIT
+Macromolecule #17: NI2M SUBUNIT
+Macromolecule #18: NESM SUBUNIT
+Macromolecule #19: NUPM SUBUNIT
+Macromolecule #20: NB6M SUBUNIT
+Macromolecule #21: NUXM SUBUNIT
+Macromolecule #22: NUYM SUBUNIT
+Macromolecule #23: NUZM SUBUNIT
+Macromolecule #24: NIAM SUBUNIT
+Macromolecule #25: NEBM SUBUNIT
+Macromolecule #26: NB2M SUBUNIT
+Macromolecule #27: NIDM SUBUNIT
+Macromolecule #28: NUUM SUBUNIT
+Macromolecule #29: NI8M SUBUNIT
+Macromolecule #30: NI9M SUBUNIT
+Macromolecule #31: N7BM SUBUNIT
+Macromolecule #32: UNKNOWN SUBUNIT
+Macromolecule #33: NB5M SUBUNIT
+Macromolecule #34: NUNM SUBUNIT
+Macromolecule #35: ND1 SUBUNIT (NU1M)
+Macromolecule #36: ND2 SUBUNIT (NU2M)
+Macromolecule #37: ND3 SUBUNIT (NU3M)
+Macromolecule #38: ND4 SUBUNIT (NU4M)
+Macromolecule #39: ND5 SUBUNIT (NU5M)
+Macromolecule #40: ND6 SUBUNIT (NU6M)
+Macromolecule #41: NB8M SUBUNIT
+Macromolecule #42: NIPM SUBUNIT
+Macromolecule #43: IRON/SULFUR CLUSTER
+Macromolecule #44: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #45: FLAVIN MONONUCLEOTIDE
+Macromolecule #46: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #47: ZINC ION
+Macromolecule #48: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #49: CARDIOLIPIN
+Macromolecule #50: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.2 Component:
| |||||||||||||||
Grid | Model: C-flat-1/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3110 / Average exposure time: 8.0 sec. / Average electron dose: 60.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 45872 / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.0015 µm / Nominal magnification: 200000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
---|---|
Output model | PDB-6gcs: |