[English] 日本語
Yorodumi- EMDB-15865: Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15865 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) from respiratory supercomplex of Tetrahymena thermophila | |||||||||||||||
Map data | Sharpened mask refined map | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding ...lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / NADH dehydrogenase activity / chloroplast thylakoid membrane / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrion organization / fatty acid metabolic process / mitochondrial membrane / electron transport chain / phospholipid binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / ribosome / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / mitochondrion / membrane / metal ion binding / cytosol 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
| |||||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15865.map.gz | 398.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15865-v30.xml emd-15865.xml | 91.9 KB 91.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15865_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_15865.png | 117.7 KB | ||
Masks | emd_15865_msk_1.map | 421.9 MB | Mask map | |
Others | emd_15865_additional_1.map.gz emd_15865_half_map_1.map.gz emd_15865_half_map_2.map.gz | 213.6 MB 391 MB 391 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15865 | HTTPS FTP |
-Validation report
Summary document | emd_15865_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_15865_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_15865_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | emd_15865_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15865 | HTTPS FTP |
-Related structure data
Related structure data | 8b6fMC 8b6gC 8b6hC 8b6jC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_15865.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened mask refined map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_15865_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened mask refined map
File | emd_15865_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened mask refined map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map A
File | emd_15865_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map B
File | emd_15865_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : NADH:ubiquinone oxidoreductase complex (complex-I) from respirato...
+Supramolecule #1: NADH:ubiquinone oxidoreductase complex (complex-I) from respirato...
+Macromolecule #1: Lipid-A-disaccharide synthase
+Macromolecule #2: NAD-dependent epimerase/dehydratase family protein
+Macromolecule #3: DnaJ domain protein
+Macromolecule #4: Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
+Macromolecule #5: RNase III domain-containing protein
+Macromolecule #6: 37S ribosomal protein S25, mitochondrial
+Macromolecule #7: Transmembrane protein, putative
+Macromolecule #8: CX9C domain-containing protein
+Macromolecule #9: NDUTT15
+Macromolecule #10: Transmembrane protein, putative
+Macromolecule #11: NADH dehydrogenase subunit 5
+Macromolecule #12: NADH-ubiquinone oxidoreductase 75 kDa subunit
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #15: NADH dehydrogenase subunit 7
+Macromolecule #16: Ymf65
+Macromolecule #17: Transcription factor apfi protein, putative
+Macromolecule #18: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #19: NADH-ubiquinone oxidoreductase 24 kDa subunit
+Macromolecule #20: Ymf62
+Macromolecule #21: Gamma-carbonic anhydrase
+Macromolecule #22: NADH-ubiquinone oxidoreductase 1, chain, putative
+Macromolecule #23: Gamma-carbonic anhydrase
+Macromolecule #24: ETC complex I subunit motif protein
+Macromolecule #25: NADH dehydrogenase subunit 9
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #28: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #29: NADH dehydrogenase, putative
+Macromolecule #30: NADH dehydrogenase subunit 10
+Macromolecule #31: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
+Macromolecule #32: Acyl carrier protein
+Macromolecule #33: Acyl carrier protein
+Macromolecule #34: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #35: Ymf58
+Macromolecule #36: Ribosomal protein L51/S25/CI-B8 domain protein
+Macromolecule #37: Transmembrane protein, putative
+Macromolecule #38: ATP synthase subunit e, mitochondrial
+Macromolecule #39: GRAM domain protein
+Macromolecule #40: Transmembrane protein, putative
+Macromolecule #41: Transmembrane protein, putative
+Macromolecule #42: Transmembrane protein, putative
+Macromolecule #43: ND1b
+Macromolecule #44: Transmembrane protein
+Macromolecule #45: Transmembrane protein, putative
+Macromolecule #46: NDUB8
+Macromolecule #47: Transmembrane protein, putative
+Macromolecule #48: NDUPH2
+Macromolecule #49: NDUB10
+Macromolecule #50: NDUA13
+Macromolecule #51: NADH dehydrogenase subunit 2
+Macromolecule #52: 2 iron, 2 sulfur cluster-binding protein
+Macromolecule #53: Thioredoxin
+Macromolecule #54: COX assembly mitochondrial protein
+Macromolecule #55: Transmembrane protein, putative
+Macromolecule #56: Transmembrane protein, putative
+Macromolecule #57: PH domain-containing protein
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #59: NDUB6
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #61: Zinc-finger protein
+Macromolecule #62: NDUB4
+Macromolecule #63: NDUB15
+Macromolecule #64: NDUTT16
+Macromolecule #65: NDUTT17
+Macromolecule #66: CHCH domain-containing protein
+Macromolecule #67: Transmembrane protein, putative
+Macromolecule #68: Ymf57
+Macromolecule #69: Complex I-MNLL
+Macromolecule #70: CARDIOLIPIN
+Macromolecule #71: URIDINE-5'-DIPHOSPHATE
+Macromolecule #72: MAGNESIUM ION
+Macromolecule #73: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #74: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #75: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #76: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
+Macromolecule #77: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #78: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #79: IRON/SULFUR CLUSTER
+Macromolecule #80: FLAVIN MONONUCLEOTIDE
+Macromolecule #81: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #82: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |