+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30676 | |||||||||
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Title | Activity optimized complex I (closed form) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly ...Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity / deoxynucleoside kinase activity / cellular respiration / ubiquinone-6 biosynthetic process / Neutrophil degranulation / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / regulation of mitochondrial membrane potential / fatty acid binding / mitochondrial membrane / apoptotic signaling pathway / electron transport chain / regulation of protein phosphorylation / mitochondrial intermembrane space / brain development / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / structural constituent of ribosome / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_30676.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-30676-v30.xml emd-30676.xml | 55 KB 55 KB | Display Display | EMDB header |
Images | emd_30676.png | 119 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 | 337.1 KB | Display | EMDB validaton report |
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Full document | emd_30676_full_validation.pdf.gz | 336.7 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 (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_30676.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-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 |
-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 |
-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: 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) |