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Yorodumi- EMDB-28011: III2IV respiratory supercomplex from Saccharomyces cerevisiae car... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28011 | |||||||||
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Title | III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant | |||||||||
Map data | Final density map | |||||||||
Sample |
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Function / homology | Function and homology information mitochondrial cytochrome c oxidase assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respirasome assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...mitochondrial cytochrome c oxidase assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respirasome assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / cellular respiration / 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 / mitochondrial crista / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Hryc CF / Mileykovskaya E / Baker M / Dowhan W | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex. Authors: Corey F Hryc / Venkata K P S Mallampalli / Evgeniy I Bovshik / Stavros Azinas / Guizhen Fan / Irina I Serysheva / Genevieve C Sparagna / Matthew L Baker / Eugenia Mileykovskaya / William Dowhan / Abstract: Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of ...Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of this lipid-protein interaction is still lacking. To address the essential role of cardiolipin in supercomplex organization, we report cryo-EM structures of a wild type supercomplex (IVIIIIV) and a supercomplex (IIIIV) isolated from a cardiolipin-lacking Saccharomyces cerevisiae mutant at 3.2-Å and 3.3-Å resolution, respectively, and demonstrate that phosphatidylglycerol in IIIIV occupies similar positions as cardiolipin in IVIIIIV. Lipid-protein interactions within these complexes differ, which conceivably underlies the reduced level of IVIIIIV and high levels of IIIIV and free III and IV in mutant mitochondria. Here we show that anionic phospholipids interact with positive amino acids and appear to nucleate a phospholipid domain at the interface between the individual complexes, which dampen charge repulsion and further stabilize interaction, respectively, between individual complexes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28011.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-28011-v30.xml emd-28011.xml | 38.6 KB 38.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28011_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_28011.png | 140.4 KB | ||
Masks | emd_28011_msk_1.map | 178 MB | Mask map | |
Others | emd_28011_half_map_1.map.gz emd_28011_half_map_2.map.gz | 107 MB 107 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28011 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28011 | HTTPS FTP |
-Related structure data
Related structure data | 8ec0MC 8e7sC 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_28011.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final density map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28011_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_28011_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_28011_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : III2-IV mitochondrial respiratory supercomplex
+Supramolecule #1: III2-IV mitochondrial respiratory supercomplex
+Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #4: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit 7, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #7: Cytochrome b-c1 complex subunit 8, mitochondrial
+Macromolecule #8: Cytochrome b
+Macromolecule #9: Cytochrome c oxidase subunit 1
+Macromolecule #10: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #11: Cytochrome c oxidase subunit 8, mitochondrial
+Macromolecule #12: Cytochrome c oxidase subunit 7, mitochondrial
+Macromolecule #13: Cytochrome c oxidase subunit 3
+Macromolecule #14: Cytochrome c oxidase subunit 2
+Macromolecule #15: Cytochrome c oxidase subunit 6, mitochondrial
+Macromolecule #16: Cytochrome c oxidase subunit 9, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 13, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 4, mitochondrial
+Macromolecule #19: Cytochrome c oxidase subunit 12, mitochondrial
+Macromolecule #20: Cytochrome c oxidase subunit 26, mitochondrial
+Macromolecule #21: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #22: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
+Macromolecule #23: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #25: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
+Macromolecule #26: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #27: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+Macromolecule #28: COPPER (II) ION
+Macromolecule #29: HEME-A
+Macromolecule #30: 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: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-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: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 360 pixel / Digitization - Dimensions - Height: 360 pixel / Digitization - Frames/image: 1-35 / Number real images: 20253 / Average electron dose: 49.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |