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Yorodumi- PDB-3gqf: Structural and Biophysical Properties of the Pathogenic SOD1 Vari... -
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-Basic information
Entry | Database: PDB / ID: 3gqf | ||||||
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Title | Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / HUMAN CU-ZN SUPEROXIDE DISMUTASE / SUPEROXIDE ACCEPTOR / FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS MUTANT / Acetylation / Amyotrophic lateral sclerosis / Antioxidant / Copper / Cytoplasm / Disease mutation / Disulfide bond / Metal-binding / Phosphoprotein / Ubl conjugation / Zinc | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / : / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / positive regulation of superoxide anion generation / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / placenta development / locomotory behavior / determination of adult lifespan / sensory perception of sound / regulation of blood pressure / negative regulation of inflammatory response / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / Platelet degranulation / peroxisome / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Winkler, D.D. / Schuermann, J.P. / Hart, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and biophysical properties of the pathogenic SOD1 variant H46R/H48Q. Authors: Winkler, D.D. / Schuermann, J.P. / Cao, X. / Holloway, S.P. / Borchelt, D.R. / Carroll, M.C. / Proescher, J.B. / Culotta, V.C. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gqf.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gqf.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gqf_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 3gqf_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 3gqf_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 3gqf_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/3gqf ftp://data.pdbj.org/pub/pdb/validation_reports/gq/3gqf | HTTPS FTP |
-Related structure data
Related structure data | 1azvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | DIMER |
-Components
#1: Protein | Mass: 15836.590 Da / Num. of mol.: 6 / Mutation: H46R, H48Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: UniProt: P00441, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.15 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 5, 2007 / Details: mirrors |
Radiation | Monochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 79657 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7908 / Rsym value: 0.503 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AZV Resolution: 2.2→28.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.667 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→28.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.255 Å / Total num. of bins used: 20
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