+Open data
-Basic information
Entry | Database: PDB / ID: 8ugf | ||||||
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Title | In-situ complex III, state III | ||||||
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 Respiratory electron transport / mitochondrial respiratory chain complex IV / Mitochondrial protein degradation / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane ...Respiratory electron transport / mitochondrial respiratory chain complex IV / Mitochondrial protein degradation / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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 | 8ugf.cif.gz | 770.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ugf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ugf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ugf_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 8ugf_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 8ugf_validation.xml.gz | 133.9 KB | Display | |
Data in CIF | 8ugf_validation.cif.gz | 191.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugf ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugf | HTTPS FTP |
-Related structure data
Related structure data | 42223MC 8ud1C 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 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
-Cytochrome b-c1 complex subunit ... , 7 types, 16 molecules 3A3N3B3O3E3I3R3V3F3S3G3T3H3U3X3Y
#1: Protein | Mass: 52756.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0PK14 #2: Protein | Mass: 48262.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RPD2 #5: Protein | Mass: 29492.600 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480EHC1 #6: Protein | Mass: 13587.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZPR8 #7: Protein | Mass: 9784.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0SHY6 #8: Protein | Mass: 10685.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1JI21 #10: Protein | Mass: 6560.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2 |
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-Protein , 3 types, 6 molecules 3C3P3D3Q3J3W
#3: Protein | Mass: 42840.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9 #4: Protein | Mass: 35359.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UNI7 #9: Protein | Mass: 7412.530 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1J3N6 |
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-Non-polymers , 7 types, 32 molecules
#11: Chemical | ChemComp-CDL / #12: Chemical | ChemComp-3PE / #13: Chemical | ChemComp-HEM / #14: Chemical | ChemComp-U10 / #15: Chemical | #16: Chemical | #17: 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: 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-#3, #6-#10 / 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT | ||||||||||||||||||||||||
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