+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40566 | |||||||||
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Title | human liver mitochondrial Superoxide dismutase [Mn] | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human / liver / mitochondrial / Superoxide dismutase [Mn] / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / positive regulation of vascular associated smooth muscle cell apoptotic process / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / negative regulation of vascular associated smooth muscle cell proliferation / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / response to zinc ion / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / hemopoiesis / response to immobilization stress / response to axon injury / response to hyperoxia / neuron development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / respiratory electron transport chain / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / liver development / regulation of mitochondrial membrane potential / response to activity / locomotory behavior / response to gamma radiation / regulation of blood pressure / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / multicellular organismal-level iron ion homeostasis / oxygen binding / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Zhang Z / Tringides M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell Proteomics / Year: 2023 Title: High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Authors: Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu / Abstract: The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40566.map.gz | 32.3 MB | EMDB map data format | |
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Header (meta data) | emd-40566-v30.xml emd-40566.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40566_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_40566.png | 144.3 KB | ||
Filedesc metadata | emd-40566.cif.gz | 4.9 KB | ||
Others | emd_40566_half_map_1.map.gz emd_40566_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40566 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40566 | HTTPS FTP |
-Validation report
Summary document | emd_40566_validation.pdf.gz | 796 KB | Display | EMDB validaton report |
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Full document | emd_40566_full_validation.pdf.gz | 795.6 KB | Display | |
Data in XML | emd_40566_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_40566_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40566 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40566 | HTTPS FTP |
-Related structure data
Related structure data | 8sksMC 8sgpC 8sgrC 8sgsC 8sgvC 8shsC 8sk6C 8sk8C 8skrC 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_40566.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #1
File | emd_40566_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40566_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Superoxide dismutase [Mn]
Entire | Name: Superoxide dismutase [Mn] |
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Components |
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-Supramolecule #1: Superoxide dismutase [Mn]
Supramolecule | Name: Superoxide dismutase [Mn] / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Superoxide dismutase [Mn], mitochondrial
Macromolecule | Name: Superoxide dismutase [Mn], mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: superoxide dismutase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.782119 KDa |
Sequence | String: MLSRAVCGTS RQLAPVLGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN NLNVTEEKYQ EALAKGDVTA QIALQPALK FNGGGHINHS IFWTNLSPNG GGEPKGELLE AIKRDFGSFD KFKEKLTAAS VGVQGSGWGW LGFNKERGHL Q IAACPNQD ...String: MLSRAVCGTS RQLAPVLGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN NLNVTEEKYQ EALAKGDVTA QIALQPALK FNGGGHINHS IFWTNLSPNG GGEPKGELLE AIKRDFGSFD KFKEKLTAAS VGVQGSGWGW LGFNKERGHL Q IAACPNQD PLQGTTGLIP LLGIDVWEHA YYLQYKNVRP DYLKAIWNVI NWENVTERYM ACKK UniProtKB: Superoxide dismutase [Mn], mitochondrial |
-Macromolecule #2: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.5 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |