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- EMDB-27940: III2IV2 respiratory supercomplex from Saccharomyces cerevisiae wi... -
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Open data
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Basic information
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Title | III2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6 | |||||||||
![]() | Final Density Map | |||||||||
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Function / homology | ![]() matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Hryc CF / Mileykovskaya E / Baker M / Dowhan W | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 136.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 39.4 KB 39.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.4 KB | Display | ![]() |
Images | ![]() | 168.1 KB | ||
Others | ![]() ![]() | 134.1 MB 134.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 876.1 KB | Display | ![]() |
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Full document | ![]() | 875.6 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e7sMC ![]() 8ec0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
-Half map: Half map B
File | emd_27940_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_27940_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
+Entire : III2-IV2 mitochondrial respiratory supercomplex
+Supramolecule #1: III2-IV2 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 10, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7, mitochondrial
+Macromolecule #7: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #8: Cytochrome b-c1 complex subunit 8, mitochondrial
+Macromolecule #9: Cytochrome b
+Macromolecule #10: Cytochrome c oxidase subunit 1
+Macromolecule #11: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #12: Cytochrome c oxidase subunit 8, mitochondrial
+Macromolecule #13: Cytochrome c oxidase subunit 7, mitochondrial
+Macromolecule #14: Cytochrome c oxidase subunit 3
+Macromolecule #15: Cytochrome c oxidase subunit 2
+Macromolecule #16: Cytochrome c oxidase subunit 6, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 9, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 13, mitochondrial
+Macromolecule #19: Cytochrome c oxidase subunit 4, mitochondrial
+Macromolecule #20: Cytochrome c oxidase subunit 12, mitochondrial
+Macromolecule #21: Cytochrome c oxidase subunit 26, mitochondrial
+Macromolecule #22: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #23: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
+Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #25: CARDIOLIPIN
+Macromolecule #26: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
+Macromolecule #27: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-penta...
+Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #29: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+Macromolecule #30: HEME-A
+Macromolecule #31: COPPER (II) ION
+Macromolecule #32: DINUCLEAR COPPER ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |