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Yorodumi- PDB-2vr7: Crystal Structure of G85R ALS mutant of Human Cu,Zn Superoxide Di... -
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-Basic information
Entry | Database: PDB / ID: 2vr7 | ||||||
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Title | Crystal Structure of G85R ALS mutant of Human Cu,Zn Superoxide Dismutase (CuZnSOD) at 1.58 A resolution | ||||||
Components | SUPEROXIDE DISMUTASE [CU-ZN] | ||||||
Keywords | OXIDOREDUCTASE / ZINC / COPPER / HUMAN CU / CYTOPLASM / ACETYLATION / UBL CONJUGATION / DISEASE MUTATION / ZN SUPEROXIDE DISMUTASE / AMYOTROPHIC LATERAL SCLEROSIS / ANTIOXIDANT / METAL-BINDING | ||||||
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 / glutathione metabolic process / axon cytoplasm / 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 / locomotory behavior / regulation of mitochondrial membrane potential / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Antonyuk, S. / Cao, X. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Tiwari, A. / Hayward, L.J. ...Antonyuk, S. / Cao, X. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Selverstone Valentine, J. / Hasnain, S.S. / Hart, P.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structures of the G85R Variant of Sod1 in Familial Amyotrophic Lateral Sclerosis. Authors: Cao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / ...Authors: Cao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Hasnain, S.S. / Hart, P.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vr7.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vr7.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vr7 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vr7 | HTTPS FTP |
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-Related structure data
Related structure data | 2vr6C 2vr8C 3cqpC 3cqqC 2c9sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AF
#1: Protein | Mass: 15953.741 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-154 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase |
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-Non-polymers , 5 types, 638 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-SCN / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | G85R MUTANT | |
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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: 2.4 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 20% PEG3350, 0.2M SODIUM THIOCYANATE, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 25, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→20 Å / Num. obs: 38696 / % possible obs: 93.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 8.2 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C9S Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.158 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.08 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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