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Yorodumi- PDB-8ud1: High resolution in-situ structure of complex I in respiratory sup... -
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-Basic information
Entry | Database: PDB / ID: 8ud1 | |||||||||
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Title | High resolution in-situ structure of complex I in respiratory supercomplex (composite) | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein | |||||||||
Function / homology | Function and homology information RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / ubiquinone-6 biosynthetic process / Mitochondrial protein degradation / cardiac muscle tissue development / oxidoreductase activity, acting on NAD(P)H / cellular respiration / ubiquinone binding ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / ubiquinone-6 biosynthetic process / Mitochondrial protein degradation / cardiac muscle tissue development / oxidoreductase activity, acting on NAD(P)H / cellular respiration / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / 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 / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / brain development / regulation of protein phosphorylation / negative regulation of cell growth / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / mitochondrial matrix / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Zheng, W. / Zhu, J. / Zhang, K. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: High-resolution in situ structures of mammalian respiratory supercomplexes. Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang / Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ud1.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ud1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ud1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ud1_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8ud1_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8ud1_validation.xml.gz | 195.8 KB | Display | |
Data in CIF | 8ud1_validation.cif.gz | 326.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/8ud1 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/8ud1 | HTTPS FTP |
-Related structure data
Related structure data | 42143MC 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 8ughC 8ugiC 8ugjC 8ugkC 8uglC 8ugnC 8ugpC 8ugrC 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 1A1H1J1K1L1M1N
#1: Protein | Mass: 13026.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 35619.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: A0A0U1RS44, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882 |
#11: Protein | Mass: 10855.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 68723.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 51887.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 39105.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 1B1C1D1I1Q1R1e
#2: Protein | Mass: 28500.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VVS8 |
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#3: Protein | Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4 |
#4: Protein | Mass: 52953.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1TTB3 |
#9: Protein | Mass: 27135.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZUN9 |
#17: Protein | Mass: 19746.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SN37 |
#18: Protein | Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1THU2 |
#30: Protein | Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VX77 |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 1E1F1s
#5: Protein | Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VRV3 |
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#6: Protein | Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SZP7 |
#44: Protein | Mass: 48217.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TE42 |
-Protein , 1 types, 1 molecules 1G
#7: Protein | Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ARY3 |
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-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 10 molecules 1O1S1V1W1X1Y1a1b1q1r
#15: Protein | Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9 |
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#19: Protein | Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1FN21 |
#21: Protein | Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0UWW0 |
#22: Protein | Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480VKQ8 |
#23: Protein | Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K6B5 |
#24: Protein | Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4 |
#26: Protein | Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0TJQ4 |
#27: Protein | Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VQ42 |
#42: Protein | Mass: 17162.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4 |
#43: Protein | Mass: 12690.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8W4F7N8 |
-NADH:ubiquinone oxidoreductase subunit ... , 4 types, 5 molecules 1P1T1U1Z1j
#16: Protein | Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULW2 | ||||
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#20: Protein | Mass: 17338.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1KH26 #25: Protein | | Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K655 #35: Protein | | Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1G9F4 |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules 1c1d
#28: Protein | Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYQ2 |
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#29: Protein | Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3 |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules 1f1g1h1i1k1l1m1n1o1p
#31: Protein | Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SNY5 |
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#32: Protein | Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7 |
#33: Protein | Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6 |
#34: Protein | Mass: 15645.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UIV8 |
#36: Protein | Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VD84 |
#37: Protein | Mass: 21658.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B8Y651 |
#38: Protein | Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0 |
#39: Protein | Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5 |
#40: Protein | Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1 |
#41: Protein | Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0R7A9 |
-Non-polymers , 14 types, 4320 molecules
#45: Chemical | ChemComp-PC1 / #46: Chemical | ChemComp-SF4 / #47: Chemical | #48: Chemical | ChemComp-FMN / | #49: Chemical | ChemComp-K / | #50: Chemical | ChemComp-3PE / #51: Chemical | ChemComp-CDL / #52: Chemical | ChemComp-GTP / | #53: Chemical | ChemComp-MG / | #54: Chemical | ChemComp-NDP / | #55: Chemical | ChemComp-ZN / | #56: Chemical | #57: Chemical | ChemComp-MYR / | #58: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 3000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113902 / Symmetry type: POINT | ||||||||||||||||||||||||
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