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Yorodumi- PDB-8ugr: In-situ structure of typeX supercomplex in respiratory chain (com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ugr | ||||||
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Title | In-situ structure of typeX supercomplex 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 / deoxynucleoside kinase activity / cellular respiration / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / 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 / enzyme regulator activity / 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 / mitochondrial intermembrane space / brain development / 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 / oxidoreductase activity / electron transfer activity / nuclear body / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 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 | 8ugr.cif.gz | 5.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ugr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ugr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ugr_validation.pdf.gz | 7.4 MB | Display | wwPDB validaton report |
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Full document | 8ugr_full_validation.pdf.gz | 7.7 MB | Display | |
Data in XML | 8ugr_validation.xml.gz | 697.1 KB | Display | |
Data in CIF | 8ugr_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugr ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugr | HTTPS FTP |
-Related structure data
Related structure data | 42233MC 8ud1C 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 8ughC 8ugiC 8ugjC 8ugkC 8uglC 8ugnC 8ugpC 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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-Components
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 14 molecules 1A5A1H5H1J5J1K5K1L5L1M5M1N5N
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 14 molecules 1B5B1C5C1D5D1I5I1Q5Q1R5R1e5e
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 6 molecules 1E5E1F5F1s5s
+Protein , 4 types, 14 molecules 1G5G3C3P6C6P3D3Q6D6Q3J3W6J6W
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 20 molecules 1O5O1S5S1V5V1W5W1X5X1Y5Y1a5a1b5b1q5q1r5r
+NADH:ubiquinone oxidoreductase subunit ... , 4 types, 10 molecules 1P5P1T1U5T5U1Z5Z1j5j
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 4 molecules 1c5c1d5d
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 20 molecules 1f5f1g5g1h5h1i5i1k5k1l5l1m5m1n5n1o5o1p5p
+Cytochrome b-c1 complex subunit ... , 7 types, 32 molecules 3A3N6A6N3B3O6B6O3E3I3R3V6E6I6R6V3F3S6F6S3G3T6G6T3H3U6H6U3X3Y6X6Y
+Cytochrome c oxidase subunit ... , 14 types, 28 molecules 4A8A4B8B4C8C4D8D4E8E4F8F4G8G4H8H4I8I4J8J4K8K4L8L4M8M4N8N
+Non-polymers , 25 types, 190 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-#68 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofaSus 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: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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