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Yorodumi- EMDB-15867: Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from... -
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-Basic information
Entry | Database: EMDB / ID: EMD-15867 | |||||||||||||||
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Title | Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / mitochondrial respiratory chain complex IV / cytochrome-c oxidase ...thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / antiporter activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Golgi organization / transmembrane transporter activity / endoplasmic reticulum-Golgi intermediate compartment / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport / mitochondrial inner membrane / copper ion binding / DNA-binding transcription factor activity / heme binding / endoplasmic reticulum / mitochondrion / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) / Tetrahymena thermophila SB210 (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 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_15867.map.gz | 391.8 MB | EMDB map data format | |
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Header (meta data) | emd-15867-v30.xml emd-15867.xml | 74.1 KB 74.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15867_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_15867.png | 94.8 KB | ||
Masks | emd_15867_msk_1.map | 421.9 MB | Mask map | |
Others | emd_15867_half_map_1.map.gz emd_15867_half_map_2.map.gz | 391.2 MB 391.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15867 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15867 | HTTPS FTP |
-Related structure data
Related structure data | 8b6hMC 8b6fC 8b6gC 8b6jC 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_15867.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2519 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15867_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15867_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15867_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cytochrome c oxidase dimer (complex-IV) from respiratory supercom...
+Supramolecule #1: Cytochrome c oxidase dimer (complex-IV) from respiratory supercom...
+Macromolecule #1: Cytochrome c oxidase subunit 1
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: Ymf68
+Macromolecule #4: Cytochrome C oxidase subunit Vb protein
+Macromolecule #5: Transmembrane protein, putative
+Macromolecule #6: Structural protein
+Macromolecule #7: Transmembrane protein, putative
+Macromolecule #8: Transmembrane protein, putative
+Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #10: Transmembrane protein, putative
+Macromolecule #11: CTF/NF-I domain-containing protein
+Macromolecule #12: Transmembrane protein, putative
+Macromolecule #13: Ymf67
+Macromolecule #14: Protein phosphatase 2C, putative
+Macromolecule #15: SURF1-like protein
+Macromolecule #16: TraB family protein
+Macromolecule #17: Transmembrane protein, putative
+Macromolecule #18: Oxoglutarate/malate translocator protein, putative
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mit...
+Macromolecule #20: Carrier protein
+Macromolecule #21: 2-oxoglutarate/malate carrier protein
+Macromolecule #22: SURF1-like protein
+Macromolecule #23: COXTT9
+Macromolecule #24: COXTT10
+Macromolecule #25: 39S ribosomal protein L9, mitochondrial
+Macromolecule #26: COXTT12,Transmembrane protein,Transmembrane protein
+Macromolecule #27: Transmembrane protein, putative
+Macromolecule #28: COXTT27
+Macromolecule #29: Ymf75
+Macromolecule #30: Mobilization protein
+Macromolecule #31: Iron-binding zinc finger CDGSH type protein
+Macromolecule #32: COXTT28
+Macromolecule #33: Transmembrane protein, putative
+Macromolecule #34: Transmembrane protein
+Macromolecule #35: Decapping nuclease
+Macromolecule #36: Complex III subunit VII
+Macromolecule #37: Transmembrane protein, putative
+Macromolecule #38: Transmembrane protein, putative
+Macromolecule #39: COXTT22
+Macromolecule #40: Transmembrane protein, putative
+Macromolecule #41: Phage protein
+Macromolecule #42: Transmembrane protein, putative
+Macromolecule #43: Lysozyme
+Macromolecule #44: Ymf70
+Macromolecule #45: Zf-Tim10_DDP domain-containing protein
+Macromolecule #46: ABC transporter
+Macromolecule #47: YflT domain-containing protein
+Macromolecule #48: Cullin domain-containing protein
+Macromolecule #49: Zf-Tim10_DDP domain-containing protein
+Macromolecule #50: Annexin
+Macromolecule #51: Transposase
+Macromolecule #52: Tim10/DDP family zinc finger protein
+Macromolecule #53: COXBP,Chromosome condensation regulator RCC1 repeat protein,Chrom...
+Macromolecule #54: HEME-A
+Macromolecule #55: COPPER (II) ION
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: CARDIOLIPIN
+Macromolecule #58: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #59: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #60: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
+Macromolecule #61: CALCIUM ION
+Macromolecule #62: DINUCLEAR COPPER ION
+Macromolecule #63: ZINC ION
+Macromolecule #64: POTASSIUM ION
+Macromolecule #65: Ubiquinone-8
+Macromolecule #66: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #67: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #68: ADENOSINE-5'-TRIPHOSPHATE
-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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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: 2.6 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 25.66 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |