+Open data
-Basic information
Entry | Database: PDB / ID: 7o3c | ||||||
---|---|---|---|---|---|---|---|
Title | Murine supercomplex CIII2CIV in the mature unlocked conformation | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / mitochondria / respiratory chain / supercomplex / OXIDOREDUCTASE / complex III / complex IV | ||||||
Function / homology | Function and homology information Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / respiratory chain complex IV assembly / pyramidal neuron development ...Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / respiratory chain complex IV assembly / pyramidal neuron development / response to mercury ion / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex IV / Mitochondrial protein degradation / : / : / response to alkaloid / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / response to copper ion / response to glucagon / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / enzyme regulator activity / ATP synthesis coupled electron transport / response to electrical stimulus / lactation / response to hormone / respiratory electron transport chain / cerebellum development / response to activity / central nervous system development / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / response to toxic substance / response to calcium ion / myelin sheath / response to ethanol / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / response to hypoxia / response to xenobiotic stimulus / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Vercellino, I. / Sazanov, L.A. | ||||||
Funding support | Austria, 1items
| ||||||
Citation | Journal: Nature / Year: 2021 Title: Structure and assembly of the mammalian mitochondrial supercomplex CIIICIV. Authors: Irene Vercellino / Leonid A Sazanov / Abstract: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is ...The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is debated. Supercomplexes CIIICIV (refs. ), CICIII (ref. ) and CICIIICIV (respirasome) exist in mammals, but in contrast to CICIII and the respirasome, to date the only known eukaryotic structures of CIIICIV come from Saccharomyces cerevisiae and plants, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIIICIV and its assembly intermediates, in different conformations. We describe the assembly of CIIICIV from the CIII precursor to the final CIIICIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. ) deep into CIII, while its C terminus is integrated into CIV. Our structures (which include CICIII and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIIICIV and has no role in the assembly of the respirasome. We show that CIII is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII, explaining the presence of one copy of CIV in CIIICIV in mammals. Finally, we show that CIII and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIIICIV in fine tuning the efficiency of electron transfer in the electron transport chain. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7o3c.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7o3c.ent.gz | 1009.7 KB | Display | PDB format |
PDBx/mmJSON format | 7o3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o3c_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7o3c_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7o3c_validation.xml.gz | 144.5 KB | Display | |
Data in CIF | 7o3c_validation.cif.gz | 205.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/7o3c ftp://data.pdbj.org/pub/pdb/validation_reports/o3/7o3c | HTTPS FTP |
-Related structure data
Related structure data | 12703MC 7o37C 7o3eC 7o3hC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Cytochrome b-c1 complex subunit ... , 9 types, 17 molecules ALBMEPFQGRHSJUKVT
#1: Protein | Mass: 49355.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CZ13 #2: Protein | Mass: 46641.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9DB77 #5: Protein | Mass: 21524.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CR68, quinol-cytochrome-c reductase #6: Protein | Mass: 13456.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CQB4 #7: Protein | Mass: 9652.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CQ69 #8: Protein | Mass: 9002.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P99028 #9: Protein | Mass: 7326.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q8R1I1 #10: Protein | Mass: 6546.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CPX8 #11: Protein | | Mass: 7900.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CR68 |
---|
-Protein , 3 types, 5 molecules CNDOI
#3: Protein | Mass: 43240.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00158 #4: Protein | Mass: 27312.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9D0M3, quinol-cytochrome-c reductase #12: Protein | | Mass: 12575.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q99KD6 |
---|
-Cytochrome c oxidase subunit ... , 12 types, 12 molecules abcdefghiklm
#13: Protein | Mass: 56945.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00397, cytochrome-c oxidase |
---|---|
#14: Protein | Mass: 25993.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00405, cytochrome-c oxidase |
#15: Protein | Mass: 29948.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00416, cytochrome-c oxidase |
#16: Protein | Mass: 17225.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P19783 |
#17: Protein | Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P12787 |
#18: Protein | Mass: 10862.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P19536 |
#19: Protein | Mass: 9437.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P43023 |
#20: Protein | Mass: 9955.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P56391 |
#21: Protein | Mass: 8352.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CPQ1 |
#22: Protein | Mass: 6317.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P56393 |
#23: Protein/peptide | Mass: 5451.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P17665 |
#24: Protein/peptide | Mass: 4660.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P48772 |
-Non-polymers , 13 types, 41 molecules
#25: Chemical | ChemComp-3PE / #26: Chemical | ChemComp-CDL / #27: Chemical | ChemComp-HEM / #28: Chemical | #29: Chemical | #30: Chemical | #31: Chemical | ChemComp-CU / | #32: Chemical | ChemComp-NA / | #33: Chemical | #34: Chemical | ChemComp-MG / | #35: Chemical | ChemComp-CUA / | #36: Chemical | ChemComp-ZN / | #37: Chemical | ChemComp-TGL / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Murine full supercomplex CIII2CIV in the unlocked conformation Type: COMPLEX Details: Dimer of Complex III, monomer of complex IV, bridged by SCAF1 Entity ID: #1-#24 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.7 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) / Strain: CD1 / Cellular location: inner mitochondrial membrane / Organ: heart / Organelle: mitochondria / Tissue: cardiac muscle | |||||||||||||||||||||||||
Buffer solution | pH: 7.7 / Details: CHAPS was added only upon freezing | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 magnification: 75000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.17 sec. / Electron dose: 90.66 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7245 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1500000 Details: multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16228 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 80 / Protocol: OTHER / Space: REAL / Target criteria: MAXIMAL LIKELYHOOD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|