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Yorodumi- PDB-1ozt: Crystal Structure of apo-H46R Familial ALS Mutant human Cu,Zn Sup... -
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-Basic information
Entry | Database: PDB / ID: 1ozt | ||||||
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Title | Crystal Structure of apo-H46R Familial ALS Mutant human Cu,Zn Superoxide Dismutase (CuZnSOD) to 2.5A resolution | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / beta barrel / amyloid-like linear filaments | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Elam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Amyloid-like Filaments and Water-filled Nanotubes Formed by SOD1 Mutant Proteins Linked to Familial ALS Authors: Elam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / 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 | 1ozt.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ozt.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ozt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ozt_validation.pdf.gz | 488.5 KB | Display | wwPDB validaton report |
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Full document | 1ozt_full_validation.pdf.gz | 509.5 KB | Display | |
Data in XML | 1ozt_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 1ozt_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1ozt ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1ozt | HTTPS FTP |
-Related structure data
Related structure data | 1oezC 1ozuC 1azvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a homodimer. There are 4 homodimers in the asymmetric unit. |
-Components
#1: Protein | Mass: 15846.607 Da / Num. of mol.: 8 / Mutation: H46R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: P00441, superoxide dismutase #2: 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: 2.59 Å3/Da / Density % sol: 52.12 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium acetate, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.989 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2000 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 40758 / Num. obs: 40758 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.44 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.32 / Num. unique all: 2719 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Num. measured all: 167752 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AZV Resolution: 2.5→42.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2446069.4 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9058 Å2 / ksol: 0.336112 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 42.4 Å / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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