+Open data
-Basic information
Entry | Database: PDB / ID: 8c8q | ||||||
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Title | Cytochrome c oxidase from Schizosaccharomyces pombe | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Electron transfer / proton transfer / respiration | ||||||
Function / homology | Function and homology information mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / mitochondrial respirasome / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / mitochondrial respirasome / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
Authors | Moe, A. / Adelroth, P. / Brzezinski, P. / Nasvik Ojemyr, L. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Commun Chem / Year: 2023 Title: Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor. Authors: Agnes Moe / Pia Ädelroth / Peter Brzezinski / Linda Näsvik Öjemyr / Abstract: Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity ...Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity purified respiratory complex IV (CIV) from S. pombe. The reaction sequence of the reduced enzyme with O proceeds over a time scale of µs-ms, similar to that of the mammalian CIV. The cryo-EM structure of CIV revealed eleven subunits as well as a bound hypoxia-induced gene 1 (Hig1) domain of respiratory supercomplex factor 2 (Rcf2). These results suggest that binding of Rcf2 does not require the presence of a CIII-CIV supercomplex, i.e. Rcf2 is a component of CIV. An AlphaFold-Multimer model suggests that the Hig1 domains of both Rcf1 and Rcf2 bind at the same site of CIV suggesting that their binding is mutually exclusive. Furthermore, the differential functional effect of Rcf1 or Rcf2 is presumably caused by interactions of CIV with their different non-Hig1 domain parts. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c8q.cif.gz | 379.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c8q.ent.gz | 302.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8q ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8q | HTTPS FTP |
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-Related structure data
Related structure data | 16491MC 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 ... , 9 types, 9 molecules ABCDFGIJK
#1: Protein | Mass: 59607.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P07657, cytochrome-c oxidase |
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#2: Protein | Mass: 28139.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P21534, cytochrome-c oxidase |
#3: Protein | Mass: 30432.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P14575, cytochrome-c oxidase |
#4: Protein | Mass: 17624.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79010 |
#6: Protein | Mass: 15958.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTF6 |
#7: Protein | Mass: 6741.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: G2TRP5 |
#9: Protein | Mass: 6652.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94705 |
#10: Protein | Mass: 10275.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94581 |
#11: Protein | Mass: 15224.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74471 |
-Cytochrome c oxidase polypeptide ... , 2 types, 2 molecules EH
#5: Protein | Mass: 24933.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: cox5, SPCC338.10c / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74988 |
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#8: Protein | Mass: 7512.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P4W1 |
-Protein / Protein/peptide , 2 types, 2 molecules LM
#12: Protein | Mass: 27084.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P3B2 |
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#13: Protein/peptide | Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) |
-Non-polymers , 7 types, 11 molecules
#14: Chemical | #15: Chemical | ChemComp-CU / | #16: Chemical | ChemComp-MG / | #17: Chemical | ChemComp-CA / | #18: Chemical | ChemComp-PEF / #19: Chemical | ChemComp-CUA / | #20: Chemical | ChemComp-ZN / | |
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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: Cytochrome c oxidase / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL |
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Molecular weight | Value: 0.246 MDa / Experimental value: NO |
Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
Buffer solution | pH: 8 |
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: C-flat-2/2 |
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 |
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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 FIELDBright-field microscopy / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127659 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.41 Å2 | ||||||||||||||||||||||||
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