+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16491 | |||||||||
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Title | Cytochrome c oxidase from Schizosaccharomyces pombe | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Mitochondrial protein degradation / mitochondrial cytochrome c oxidase assembly / : / cytochrome-c oxidase / : / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity ...Mitochondrial protein degradation / mitochondrial cytochrome c oxidase assembly / : / cytochrome-c oxidase / : / 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) / fission yeast (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Moe A / Adelroth P / Brzezinski P / Nasvik Ojemyr L | |||||||||
Funding support | Sweden, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16491.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-16491-v30.xml emd-16491.xml | 27.4 KB 27.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16491_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_16491.png | 143.5 KB | ||
Others | emd_16491_half_map_1.map.gz emd_16491_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16491 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16491 | HTTPS FTP |
-Validation report
Summary document | emd_16491_validation.pdf.gz | 973.4 KB | Display | EMDB validaton report |
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Full document | emd_16491_full_validation.pdf.gz | 972.9 KB | Display | |
Data in XML | emd_16491_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_16491_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16491 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16491 | HTTPS FTP |
-Related structure data
Related structure data | 8c8qMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16491.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8617 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16491_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16491_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cytochrome c oxidase
+Supramolecule #1: Cytochrome c oxidase
+Macromolecule #1: Cytochrome c oxidase subunit 1
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: Cytochrome c oxidase subunit 3
+Macromolecule #4: Cytochrome c oxidase subunit 4, mitochondrial
+Macromolecule #5: Cytochrome c oxidase polypeptide 5, mitochondrial
+Macromolecule #6: Cytochrome c oxidase subunit 6, mitochondrial
+Macromolecule #7: Cytochrome c oxidase subunit 7
+Macromolecule #8: Cytochrome c oxidase polypeptide VIII, mitochondrial
+Macromolecule #9: Cytochrome c oxidase subunit 9, mitochondrial
+Macromolecule #10: Cytochrome c oxidase subunit 12, mitochondrial
+Macromolecule #11: Cytochrome c oxidase subunit 13, mitochondrial
+Macromolecule #12: Respiratory supercomplex factor 2 homolog C1565.01
+Macromolecule #13: Unknown polypeptide
+Macromolecule #14: HEME-A
+Macromolecule #15: COPPER (II) ION
+Macromolecule #16: MAGNESIUM ION
+Macromolecule #17: CALCIUM ION
+Macromolecule #18: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
+Macromolecule #19: DINUCLEAR COPPER ION
+Macromolecule #20: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |