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Yorodumi- EMDB-52619: High resolution Cryo-EM structure of human complex I in mitochondria -
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Open data
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Basic information
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| Title | High resolution Cryo-EM structure of human complex I in mitochondria | |||||||||
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Keywords | Human mitochondria / respirasome complex / complex I / NADH dehydrogenase / MEMBRANE PROTEIN | |||||||||
| Function / homology | Function and homology informationprotein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / protein insertion into mitochondrial inner membrane / ubiquinone biosynthetic process / blastocyst hatching / cellular respiration / cellular response to oxygen levels ...protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / protein insertion into mitochondrial inner membrane / ubiquinone biosynthetic process / blastocyst hatching / cellular respiration / cellular response to oxygen levels / response to light intensity / mesenchymal stem cell proliferation / Mitochondrial protein import / reproductive system development / iron-sulfur cluster assembly complex / respiratory chain complex / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / mesenchymal stem cell differentiation / circulatory system development / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / negative regulation of non-canonical NF-kappaB signal transduction / cardiac muscle tissue development / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / positive regulation of mitochondrial membrane potential / response to hydroperoxide / azurophil granule membrane / cellular response to glucocorticoid stimulus / stem cell division / NADH dehydrogenase activity / iron-sulfur cluster assembly / sodium ion transport / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / regulation of protein phosphorylation / positive regulation of ATP biosynthetic process / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / RHOG GTPase cycle / respiratory chain complex I / response to cAMP / positive regulation of execution phase of apoptosis / NADH dehydrogenase (ubiquinone) activity / endopeptidase activator activity / quinone binding / cellular response to interferon-beta / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / neurogenesis / ionotropic glutamate receptor binding / Mitochondrial protein degradation / substantia nigra development / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / synaptic membrane / cerebellum development / fatty acid binding / regulation of mitochondrial membrane potential / respiratory electron transport chain / response to nicotine / DNA damage response, signal transduction by p53 class mediator / kidney development / response to hydrogen peroxide / monooxygenase activity / sensory perception of sound / fatty acid metabolic process / circadian rhythm / brain development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / NAD binding / positive regulation of protein catabolic process / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / protease binding / response to ethanol / gene expression / in utero embryonic development / response to hypoxia / electron transfer activity / mitochondrial inner membrane / nuclear speck / nuclear body / mitochondrial matrix Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.63 Å | |||||||||
Authors | Nguyen MD / Singh V / Rorbach J | |||||||||
| Funding support | Sweden, 1 items
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Citation | Journal: To Be PublishedTitle: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome Authors: Nguyen MD / Singh V / Rorbach J | |||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_52619.map.gz | 211 MB | EMDB map data format | |
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| Header (meta data) | emd-52619-v30.xml emd-52619.xml | 66.8 KB 66.8 KB | Display Display | EMDB header |
| Images | emd_52619.png | 102.6 KB | ||
| Filedesc metadata | emd-52619.cif.gz | 14 KB | ||
| Others | emd_52619_half_map_1.map.gz emd_52619_half_map_2.map.gz | 391.5 MB 391.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-52619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-52619 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9i4iMC ![]() 9hzlC ![]() 52596 M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_52619.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: 0.875 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #1
| File | emd_52619_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_52619_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Complex I in human mitochondria
+Supramolecule #1: Complex I in human mitochondria
+Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #3: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #4: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #6: Acyl carrier protein, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #17: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #18: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #19: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #21: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #25: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #26: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #30: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #38: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #39: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #41: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #42: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #43: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #45: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #46: CARDIOLIPIN
+Macromolecule #47: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #48: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...
+Macromolecule #49: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #50: MAGNESIUM ION
+Macromolecule #51: IRON/SULFUR CLUSTER
+Macromolecule #52: FLAVIN MONONUCLEOTIDE
+Macromolecule #53: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #54: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #55: ZINC ION
+Macromolecule #56: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.5 sec. / Average electron dose: 35.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm |
| Sample stage | Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Sweden, 1 items
Citation

















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Processing
FIELD EMISSION GUN

