+Open data
-Basic information
Entry | Database: PDB / ID: 7dh0 | ||||||
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Title | Activity optimized complex I (open form) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / respiratory / electron transport | ||||||
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 / ubiquinone-6 biosynthetic process / cellular respiration / Neutrophil degranulation / NADH dehydrogenase activity / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / ubiquinone 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 / brain development / mitochondrial intermembrane space / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 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 | 7dh0.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7dh0.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7dh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dh0 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dh0 | HTTPS FTP |
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-Related structure data
Related structure data | 30677MC 7dgqC 7dgrC 7dgsC 7dgzC 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 2345716
#1: Protein | Mass: 39274.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03892, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 13058.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03898, NADH:ubiquinone reductase (H+-translocating) |
#3: Protein | Mass: 52130.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03910, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 10800.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03902, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 19082.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03924, NADH:ubiquinone reductase (H+-translocating) |
#41: Protein | Mass: 35688.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03887, NADH:ubiquinone reductase (H+-translocating) |
#42: Protein | Mass: 68327.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P03920, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 89F
#6: Protein | Mass: 48562.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P25708, NADH:ubiquinone reductase (H+-translocating) |
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#7: Protein | Mass: 23840.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P04394, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 8451.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P25712 |
-Protein , 2 types, 3 molecules AWM
#8: Protein | Mass: 77044.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P15690, NADH:ubiquinone reductase (H+-translocating) |
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#29: Protein | Mass: 10119.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P52505 |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCDEGHI
#9: Protein | Mass: 49207.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P17694, NADH:ubiquinone reductase (H+-translocating) |
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#10: Protein | Mass: 26464.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P23709, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P42026, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P42028, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 15361.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02375 |
#15: Protein | Mass: 12563.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02379 |
#16: Protein | Mass: 10551.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23934 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules JKLNOPQRSTUV
#17: Protein | Mass: 8117.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02377 |
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#18: Protein | Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02370 |
#19: Protein | Mass: 9226.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02371 |
#20: Protein | Mass: 13203.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23935 |
#21: Protein | Mass: 14952.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02366 |
#22: Protein | Mass: 12564.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q05752 |
#23: Protein | Mass: 19992.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P42029 |
#24: Protein | Mass: 39174.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P34943 |
#25: Protein | Mass: 36739.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P34942 |
#26: Protein | Mass: 14640.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG6 |
#27: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: O97725 |
#28: Protein | Mass: 16563.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q95KV7 |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules XYZabcdfhge
#30: Protein | Mass: 6978.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02378 |
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#31: Protein | Mass: 8500.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02374 |
#32: Protein | Mass: 11029.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02365 |
#33: Protein | Mass: 15075.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P48305 |
#34: Protein | Mass: 16752.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02380 |
#35: Protein | Mass: 15418.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02367 |
#36: Protein | Mass: 16297.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02368 |
#37: Protein | Mass: 21696.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02369 |
#38: Protein | Mass: 14469.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG5 |
#43: Protein | Mass: 21000.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02373 |
#44: Protein | Mass: 18757.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02372 |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules ij
#39: Protein/peptide | Mass: 5836.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02376 |
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#40: Protein | Mass: 14117.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02827 |
-Non-polymers , 8 types, 17 molecules
#45: Chemical | #46: Chemical | ChemComp-CDL / | #47: Chemical | ChemComp-FMN / | #48: Chemical | ChemComp-SF4 / #49: Chemical | #50: Chemical | ChemComp-ZN / | #51: Chemical | ChemComp-NAP / | #52: Chemical | |
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-Details
Has ligand of interest | Y |
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-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-#44 / 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 |
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
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72302 / Symmetry type: POINT |