+Open data
-Basic information
Entry | Database: PDB / ID: 7dgq | ||||||
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Title | Activity optimized supercomplex state1 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / respiratory / electron transport | ||||||
Function / homology | Function and homology information Complex III assembly / Complex I biogenesis / Complex IV assembly / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex III ...Complex III assembly / Complex I biogenesis / Complex IV assembly / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex III / respiratory chain complex IV / cellular response to oxygen levels / regulation of oxidative phosphorylation / ubiquinone-6 biosynthetic process / Respiratory electron transport / : / mitochondrial large ribosomal subunit binding / gliogenesis / : / oxidative phosphorylation / cytochrome-c oxidase / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / oxygen sensor activity / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / Neutrophil degranulation / cytochrome-c oxidase activity / respiratory chain complex I / mitochondrial ribosome / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / ubiquinone binding / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / response to cAMP / aerobic respiration / neurogenesis / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / central nervous system development / fatty acid binding / apoptotic signaling pathway / mitochondrial membrane / electron transport chain / brain development / regulation of protein phosphorylation / negative regulation of cell growth / mitochondrial intermembrane space / metalloendopeptidase activity / 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 / mitochondrial matrix / structural constituent of ribosome / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | ||||||
Authors | Jeon, T.J. / Lee, S.G. / Yoo, S.H. / Ryu, J.H. / Kim, D.S. / Hyun, J.K. / Kim, H.M. / Ryu, S.E. | ||||||
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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dgq.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7dgq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7dgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dgq_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7dgq_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7dgq_validation.xml.gz | 285.1 KB | Display | |
Data in CIF | 7dgq_validation.cif.gz | 481.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/7dgq ftp://data.pdbj.org/pub/pdb/validation_reports/dg/7dgq | HTTPS FTP |
-Related structure data
Related structure data | 30673MC 7dgrC 7dgsC 7dgzC 7dh0C 7dkfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 3174562
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 98F
+Cytochrome c oxidase subunit ... , 13 types, 13 molecules C3C1A9A7B4A5A6C0C2B2B3A0A8
+Protein , 4 types, 7 molecules AWMmyoz
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCDEGHI
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules JKLNOPQRSTUV
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules XYZabcdfhge
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules ij
+Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules kwlxpA1qA2rA3sB7tA4uB6vB5
+Non-polymers , 14 types, 39 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: TISSUE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: supercomplex of electron transport chain complexes / Type: COMPLEX / Entity ID: #1-#68 / Source: NATURAL |
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Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48729 / Symmetry type: POINT |