+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30675 | |||||||||
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Title | Activity optimized supercomplex state3 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Complex I biogenesis / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / cellular response to oxygen levels / : ...Complex I biogenesis / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / cellular response to oxygen levels / : / mitochondrial large ribosomal subunit binding / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / : / neural precursor cell proliferation / cytochrome-c oxidase / : / [2Fe-2S] cluster assembly / oxidative phosphorylation / oxygen sensor activity / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / Neutrophil degranulation / cytochrome-c oxidase activity / NADH dehydrogenase activity / mitochondrial ribosome / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / neurogenesis / : / enzyme regulator activity / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to cAMP / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / central nervous system development / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / structural constituent of ribosome / mitochondrial matrix / copper ion binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Jeon TJ / Lee SG / Yoo SH / Ryu JH / Kim DS / Hyun JK / Kim HM / Ryu SE | |||||||||
Citation | Journal: Antioxid Redox Signal / Year: 2022 Title: 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_30675.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-30675-v30.xml emd-30675.xml | 79.6 KB 79.6 KB | Display Display | EMDB header |
Images | emd_30675.png | 98.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30675 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30675 | HTTPS FTP |
-Validation report
Summary document | emd_30675_validation.pdf.gz | 340.6 KB | Display | EMDB validaton report |
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Full document | emd_30675_full_validation.pdf.gz | 340.2 KB | Display | |
Data in XML | emd_30675_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_30675_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30675 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30675 | HTTPS FTP |
-Related structure data
Related structure data | 7dgsMC 7dgqC 7dgrC 7dgzC 7dh0C 7dkfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30675.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Sample components
+Entire : supercomplex of electron transport chain complexes
+Supramolecule #1: supercomplex of electron transport chain complexes
+Macromolecule #1: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #4: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #6: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #7: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #10: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, 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 3, mitochondrial
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #31: Acyl carrier protein, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #45: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #47: Cytochrome b
+Macromolecule #48: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #50: Cytochrome b-c1 complex subunit 7
+Macromolecule #51: Cytochrome b-c1 complex subunit 8
+Macromolecule #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #53: Cytochrome b-c1 complex subunit 10
+Macromolecule #54: Cytochrome b-c1 complex subunit 9
+Macromolecule #55: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #56: Cytochrome c oxidase subunit 1
+Macromolecule #57: Cytochrome c oxidase subunit 2
+Macromolecule #58: Cytochrome c oxidase subunit 3
+Macromolecule #59: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #60: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #61: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #62: Cytochrome c oxidase subunit 6A2, mitochondrial
+Macromolecule #63: Cytochrome c oxidase subunit 6B1
+Macromolecule #64: Cytochrome c oxidase subunit 6C
+Macromolecule #65: Cytochrome c oxidase subunit 7A1, mitochondrial
+Macromolecule #66: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #67: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #68: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #69: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #70: CARDIOLIPIN
+Macromolecule #71: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #72: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #73: FLAVIN MONONUCLEOTIDE
+Macromolecule #74: IRON/SULFUR CLUSTER
+Macromolecule #75: ZINC ION
+Macromolecule #76: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #77: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #78: HEME C
+Macromolecule #79: HEME-A
+Macromolecule #80: COPPER (II) ION
+Macromolecule #81: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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 |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 1.4) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 24810 |
Initial angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |