+Open data
-Basic information
Entry | Database: PDB / ID: 3ecu | ||||||
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Title | Crystal structure of human apo Cu,Zn Superoxide Dismutase (SOD1) | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / HUMAN SUPEROXIDE DISMUTASE / HOMODIMERIC PROTEIN / APO PROTEIN / AGGREGATION / Acetylation / Amyotrophic lateral sclerosis / Antioxidant / Copper / Cytoplasm / Disease mutation / Metal-binding / 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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / 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 / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Calderone, V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants. Authors: Banci, L. / Bertini, I. / Boca, M. / Calderone, V. / Cantini, F. / Girotto, S. / Vieru, M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Metal-free superoxide dismutase forms soluble oligomers under physiological conditions: a possible general mechanism for familial ALS. Authors: Banci, L. / Bertini, I. / Durazo, A. / Girotto, S. / Gralla, E.B. / Martinelli, M. / Valentine, J.S. / Vieru, M. / Whitelegge, J.P. #2: Journal: PLoS ONE / Year: 2008 Title: SOD1 and amyotrophic lateral sclerosis: mutations and oligomerization. Authors: Banci, L. / Bertini, I. / Boca, M. / Girotto, S. / Martinelli, M. / Valentine, J.S. / Vieru, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ecu.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ecu.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ecu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3ecu ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ecu | HTTPS FTP |
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-Related structure data
Related structure data | 3ecvC 3ecwC 1hl5S 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15827.561 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pENTR/TEV/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Origami pLysS / 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: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 289.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Apr 30, 2007 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→106 Å / Num. all: 42832 / Num. obs: 42832 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.1 / Num. unique all: 5890 / Rsym value: 0.409 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HL5 Resolution: 1.9→39.01 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.164 / SU ML: 0.146 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.182 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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