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Yorodumi- EMDB-15868: Cryo-EM structure of cytochrome bc1 complex (complex-III) from re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15868 | |||||||||||||||
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Title | Cryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory supercomplex of Tetrahymena thermophila | |||||||||||||||
Map data | Sharpened mask refined map | |||||||||||||||
Sample |
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Function / homology | Function and homology information quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / : / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity ...quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / : / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) / Tetrahymena thermophila SB210 (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Muhleip A / Kock Flygaard R / Amunts A | |||||||||||||||
Funding support | Sweden, European Union, 4 items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex. Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts / Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex Authors: Muhleip A / Flygaard RK / Haapanen O / Baradaran R / Gruhl T / Tobiasson V / Marechal A / Sharma V / Amunts A | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15868.map.gz | 398.1 MB | EMDB map data format | |
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Header (meta data) | emd-15868-v30.xml emd-15868.xml | 35.9 KB 35.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15868_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_15868.png | 79.3 KB | ||
Masks | emd_15868_msk_1.map | 421.9 MB | Mask map | |
Others | emd_15868_additional_1.map.gz emd_15868_additional_2.map.gz emd_15868_additional_3.map.gz emd_15868_half_map_1.map.gz emd_15868_half_map_2.map.gz | 213.4 MB 1.8 MB 1.8 MB 390.9 MB 390.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15868 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15868 | HTTPS FTP |
-Related structure data
Related structure data | 8b6jMC 8b6fC 8b6gC 8b6hC 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_15868.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened mask refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15868_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened mask refined map
File | emd_15868_additional_1.map | ||||||||||||
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Annotation | Unsharpened mask refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Rieske B-state map from focused classification
File | emd_15868_additional_2.map | ||||||||||||
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Annotation | Rieske B-state map from focused classification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Rieske C-state map from focused classification
File | emd_15868_additional_3.map | ||||||||||||
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Annotation | Rieske C-state map from focused classification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A
File | emd_15868_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_15868_half_map_2.map | ||||||||||||
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Annotation | Half-map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Dimeric cytochrome bc1 complex (complex-III2)
+Supramolecule #1: Dimeric cytochrome bc1 complex (complex-III2)
+Macromolecule #1: Peptidase M16 inactive domain protein
+Macromolecule #2: M16 family peptidase, putative
+Macromolecule #3: Apocytochrome b
+Macromolecule #4: Cytochrome protein c1
+Macromolecule #5: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron...
+Macromolecule #6: Ubiquinol-cytochrome C reductase hinge protein
+Macromolecule #7: UQCRTT1
+Macromolecule #8: Transmembrane protein, putative
+Macromolecule #9: Transmembrane protein, putative
+Macromolecule #10: UQCRTT3/UP1
+Macromolecule #11: Transmembrane protein, putative
+Macromolecule #12: UQCRTT2
+Macromolecule #13: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #14: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #15: CARDIOLIPIN
+Macromolecule #16: Ubiquinone-8
+Macromolecule #17: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #18: HEME C
+Macromolecule #19: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 25.66 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 |