+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18062 | |||||||||
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Title | III2-IV1 respiratory supercomplex from S. pombe | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Supercomplex / respiration / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Respiratory electron transport / mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase ...Respiratory electron transport / mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / structural molecule activity / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Moe A / Brzezinski P | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structure and function of the III-IV-cyt supercomplex. Authors: Agnes Moe / Anna-Roza Dimogkioka / Doron Rapaport / Linda Näsvik Öjemyr / Peter Brzezinski / Abstract: The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the ...The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII), via a mobile electron carrier, cytochrome . In the present study, we isolated the CIIICIV supercomplex from the fission yeast and determined its structure with bound cyt. using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn, coordinated in the CIII subunit Cor1, which is encoded by the same gene () as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIIICIV supercomplex displays proteolytic activity suggesting a dual role of CIII in . As in the supercomplex from , subunit Cox5 of CIV faces towards one CIII monomer, but in the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII respiratory system and indicates a two-dimensional cyt. diffusion mechanism within the CIII-CIV supercomplex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18062.map.gz | 483.7 MB | EMDB map data format | |
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Header (meta data) | emd-18062-v30.xml emd-18062.xml | 50.1 KB 50.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18062_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_18062.png | 89.5 KB | ||
Filedesc metadata | emd-18062.cif.gz | 10.4 KB | ||
Others | emd_18062_additional_1.map.gz emd_18062_additional_2.map.gz emd_18062_additional_3.map.gz emd_18062_additional_4.map.gz emd_18062_half_map_1.map.gz emd_18062_half_map_2.map.gz | 59.7 MB 59.7 MB 59.7 MB 59.6 MB 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18062 | HTTPS FTP |
-Related structure data
Related structure data | 8q1bMC 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_18062.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: 3DVA class 0 after heterogeneous refinement, cyt. c...
File | emd_18062_additional_1.map | ||||||||||||
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Annotation | 3DVA class 0 after heterogeneous refinement, cyt. c at position (iii) and (iv) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3DVA class 1 after heterogeneous refinement, cyt. c...
File | emd_18062_additional_2.map | ||||||||||||
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Annotation | 3DVA class 1 after heterogeneous refinement, cyt. c at position (ii) and (iv) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3DVA class 2 after heterogeneous refinement, cyt. c at position (iii)
File | emd_18062_additional_3.map | ||||||||||||
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Annotation | 3DVA class 2 after heterogeneous refinement, cyt. c at position (iii) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3DVA class 3 after heterogeneous refinement, cyt. c at position (i)
File | emd_18062_additional_4.map | ||||||||||||
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Annotation | 3DVA class 3 after heterogeneous refinement, cyt. c at position (i) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18062_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18062_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : III2-IV1 respiratory supercomplex
+Supramolecule #1: III2-IV1 respiratory supercomplex
+Macromolecule #1: Probable mitochondrial-processing peptidase subunit beta
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 6
+Macromolecule #7: Cytochrome b-c1 complex subunit 7
+Macromolecule #8: Cytochrome b-c1 complex subunit 8
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 10
+Macromolecule #11: Cytochrome c oxidase subunit 1
+Macromolecule #12: Cytochrome c oxidase subunit 2
+Macromolecule #13: Cytochrome c oxidase subunit 3
+Macromolecule #14: Cytochrome c oxidase subunit 4, mitochondrial
+Macromolecule #15: Cytochrome c oxidase polypeptide 5, mitochondrial
+Macromolecule #16: Cytochrome c oxidase subunit 6, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 7
+Macromolecule #18: Cytochrome c oxidase polypeptide VIII, mitochondrial
+Macromolecule #19: Cytochrome c oxidase subunit 9, mitochondrial
+Macromolecule #20: Cytochrome c oxidase subunit 12, mitochondrial
+Macromolecule #21: Cytochrome c oxidase subunit 13, mitochondrial
+Macromolecule #22: Respiratory supercomplex factor 2 homolog C1565.01
+Macromolecule #23: Unknown polypeptide
+Macromolecule #24: ZINC ION
+Macromolecule #25: CARDIOLIPIN
+Macromolecule #26: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
+Macromolecule #27: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
+Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #29: UBIQUINONE-10
+Macromolecule #30: HEME C
+Macromolecule #31: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #32: HEME-A
+Macromolecule #33: COPPER (II) ION
+Macromolecule #34: CALCIUM ION
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: DINUCLEAR COPPER ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |