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Yorodumi- PDB-8ugh: In-situ structure of typeA supercomplex with lipids in respirator... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ugh | ||||||
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Title | In-situ structure of typeA supercomplex with lipids in respiratory chain (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 Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / : ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / : / regulation of oxidative phosphorylation / Mitochondrial protein degradation / : / cardiac muscle tissue development / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / cellular respiration / ubiquinol-cytochrome-c reductase activity / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / NADH dehydrogenase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / 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 / : / enzyme regulator activity / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vasoconstriction / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / central nervous system development / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial intermembrane space / negative regulation of cell growth / metalloendopeptidase activity / 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 / electron transfer activity / oxidoreductase activity / nuclear body / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / plasma membrane / 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. / Zhang, K. / Zhu, J. | ||||||
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 | 8ugh.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ugh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ugh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugh ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugh | HTTPS FTP |
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-Related structure data
Related structure data | 42225MC 8ud1C 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 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
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 1B1C1D1I1Q1R1e
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 1E1F1s
+Protein , 4 types, 7 molecules 1G3C3P3D3Q3J3W
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 10 molecules 1O1S1V1W1X1Y1a1b1q1r
+NADH:ubiquinone oxidoreductase subunit ... , 4 types, 5 molecules 1P1T1U1Z1j
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules 1c1d
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules 1f1g1h1i1k1l1m1n1o1p
+Cytochrome b-c1 complex subunit ... , 7 types, 16 molecules 3A3N3B3O3E3I3R3V3F3S3G3T3H3U3X3Y
+Cytochrome c oxidase subunit ... , 14 types, 14 molecules 4A4B4C4D4E4F4G4H4I4J4K4L4M4N
+Non-polymers , 26 types, 226 molecules
+Details
-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-#39, #41-#43 / 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: 90000 / Symmetry type: POINT | ||||||||||||||||||||||||
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