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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Activity optimized complex I (closed form) | |||||||||
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Keywords | respiratory / electron transport / OXIDOREDUCTASE | |||||||||
| Function / homology | Function and homology informationComplex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly ...Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / Neutrophil degranulation / oxygen sensor activity / NADH dehydrogenase activity / Mitochondrial protein degradation / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / response to cAMP / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / neurogenesis / reactive oxygen species metabolic process / aerobic respiration / fatty acid binding / respiratory electron transport chain / electron transport chain / circadian rhythm / brain development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / fatty acid biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / apoptotic process / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Jeon TJ / Lee SG | |||||||||
Citation | Journal: Antioxid Redox Signal / Year: 2022Title: A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex. Authors: Tae Jin Jeon / Seong-Gyu Lee / Suk Hyun Yoo / Myeongbin Kim / Dabin Song / Joonghyun Ryu / Hwangseo Park / Deok-Soo Kim / Jaekyung Hyun / Ho Min Kim / Seong Eon Ryu / ![]() Abstract: Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in ... Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in physiologically relevant conditions, we conducted cryoelectron microscopy studies with supercomplexes in a lipid-preserving state. Here, we present cryoelectron microscopy structures of bovine respiratory supercomplex IIIIIV by using a lipid-preserving sample preparation. The preparation greatly enhances the intercomplex quinone transfer activity. The structures reveal large intercomplex motions that result in different shapes and sizes of the intercomplex space between complexes I and III, forming a dynamic substrate pool. Biochemical and structural analyses indicated that intercomplex phospholipids mediate the intercomplex motions. An analysis of the different classes of focus-refined complex I showed that structural switches due to quinone reduction led to the formation of a novel channel that could transfer reduced quinones to the intercomplex substrate pool. Our results indicate potential mechanism for the facilitated electron transfer involving a dynamic substrate pool and intercomplex movement by which supercomplexes play an active role in the regulation of metabolic flux and reactive oxygen species. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_30676.map.gz | 8.4 MB | EMDB map data format | |
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| Header (meta data) | emd-30676-v30.xml emd-30676.xml | 58.2 KB 58.2 KB | Display Display | EMDB header |
| Images | emd_30676.png | 119 KB | ||
| Filedesc metadata | emd-30676.cif.gz | 12.5 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30676 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30676 | HTTPS FTP |
-Validation report
| Summary document | emd_30676_validation.pdf.gz | 382.2 KB | Display | EMDB validaton report |
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| Full document | emd_30676_full_validation.pdf.gz | 381.8 KB | Display | |
| Data in XML | emd_30676_validation.xml.gz | 6 KB | Display | |
| Data in CIF | emd_30676_validation.cif.gz | 7 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30676 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30676 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7dgzMC ![]() 7dgqC ![]() 7dgrC ![]() 7dgsC ![]() 7dh0C ![]() 7dkfC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_30676.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.3973 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : supercomplex of electron transport chain complexes
+Supramolecule #1: supercomplex of electron transport chain complexes
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #4: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #29: Acyl carrier protein, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #45: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #46: CARDIOLIPIN
+Macromolecule #47: FLAVIN MONONUCLEOTIDE
+Macromolecule #48: IRON/SULFUR CLUSTER
+Macromolecule #49: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #50: ZINC ION
+Macromolecule #51: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #52: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | tissue |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
| Startup model | Type of model: NONE |
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| Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 146842 |
| Initial angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |
| Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |
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FIELD EMISSION GUN
