+Open data
-Basic information
Entry | Database: PDB / ID: 8sks | ||||||
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Title | human liver mitochondrial Superoxide dismutase [Mn] | ||||||
Components | Superoxide dismutase [Mn], mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / human / liver / mitochondrial / Superoxide dismutase [Mn] | ||||||
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 / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / negative regulation of fat cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to zinc ion / superoxide metabolic process / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / neuron development / response to axon injury / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / glutathione metabolic process / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / post-embryonic development / release of cytochrome c from mitochondria / locomotory behavior / regulation of mitochondrial membrane potential / liver development / response to activity / response to gamma radiation / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to oxidative stress / manganese ion binding / heart development / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / mitochondrial matrix / positive regulation of cell migration / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
Authors | Zhang, Z. / Tringides, M. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sks.cif.gz | 144 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sks.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 8sks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/8sks ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8sks | HTTPS FTP |
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-Related structure data
Related structure data | 40566MC 8sgpC 8sgrC 8sgsC 8sgvC 8shsC 8sk6C 8sk8C 8skrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 24782.119 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04179, superoxide dismutase #2: Chemical | ChemComp-MN / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Superoxide dismutase [Mn] / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 39.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4080: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50014 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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