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Yorodumi- PDB-8ugl: High resolution in-situ structure of complex IV in respiratory su... -
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-Basic information
Entry | Database: PDB / ID: 8ugl | ||||||
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Title | High resolution in-situ structure of complex IV in respiratory supercomplex | ||||||
Components | (Cytochrome c oxidase subunit ...) x 14 | ||||||
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 / respiratory chain complex IV / Respiratory electron transport / : / regulation of oxidative phosphorylation / Mitochondrial protein degradation / cytochrome-c oxidase ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / : / regulation of oxidative phosphorylation / Mitochondrial protein degradation / cytochrome-c oxidase / : / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / positive regulation of vasoconstriction / electron transport coupled proton transport / enzyme regulator activity / ATP synthesis coupled electron transport / central nervous system development / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 | 8ugl.cif.gz | 442 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ugl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ugl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ugl_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8ugl_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8ugl_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 8ugl_validation.cif.gz | 110.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugl ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugl | HTTPS FTP |
-Related structure data
Related structure data | 42229MC 8ud1C 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 8ughC 8ugiC 8ugjC 8ugkC 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
-Cytochrome c oxidase subunit ... , 14 types, 14 molecules 4A4B4C4D4E4F4G4H4I4J4K4L4M4N
#1: Protein | Mass: 56992.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79876 |
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#2: Protein | Mass: 26288.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q69GF7 |
#3: Protein | Mass: 29753.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35916 |
#4: Protein | Mass: 19670.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T8J9 |
#5: Protein | Mass: 16771.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34 |
#6: Protein | Mass: 13801.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q5S3G4 |
#7: Protein | Mass: 10876.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEB7 |
#8: Protein | Mass: 10204.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQT1 |
#9: Protein | Mass: 8617.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TXH1 |
#10: Protein | Mass: 9028.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8SPJ9 |
#11: Protein | Mass: 9169.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJ57 |
#12: Protein | Mass: 7358.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1W0Y2 |
#13: Protein | Mass: 7615.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQT4 |
#14: Protein | Mass: 9322.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS3 |
-Non-polymers , 12 types, 833 molecules
#15: Chemical | ChemComp-PGV / ( #16: Chemical | #17: Chemical | ChemComp-CU / | #18: Chemical | ChemComp-MG / | #19: Chemical | ChemComp-NA / | #20: Chemical | #21: Chemical | ChemComp-CUA / | #22: Chemical | ChemComp-PSC / ( | #23: Chemical | ChemComp-ZN / | #24: Chemical | #25: Chemical | ChemComp-PO4 / | #26: Water | ChemComp-HOH / | |
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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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#14 / 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: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56000 / Symmetry type: POINT | ||||||||||||||||||||||||
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