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Yorodumi- PDB-1ji9: Solution structure of the alpha-domain of mouse metallothionein-3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ji9 | ||||||
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Title | Solution structure of the alpha-domain of mouse metallothionein-3 | ||||||
Components | METALLOTHIONEIN-III | ||||||
Keywords | METAL BINDING PROTEIN / 3-10 helix / Cd-S cluster / half turn / type II turn | ||||||
Function / homology | Function and homology information : / : / : / regulation of protein glycosylation / : / Metallothioneins bind metals / : / positive regulation of oxygen metabolic process / : / positive regulation of lysosomal membrane permeability ...: / : / : / regulation of protein glycosylation / : / Metallothioneins bind metals / : / positive regulation of oxygen metabolic process / : / positive regulation of lysosomal membrane permeability / negative regulation of hydrogen peroxide catabolic process / : / regulation of response to food / : / cellular lipid catabolic process / negative regulation of oxidoreductase activity / astrocyte end-foot / leptin-mediated signaling pathway / zinc ion transport / negative regulation of cysteine-type endopeptidase activity / negative regulation of axon extension / astrocyte development / energy reserve metabolic process / detoxification of copper ion / intracellular zinc ion homeostasis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cholesterol catabolic process / cellular response to zinc ion / protein kinase activator activity / positive regulation of catalytic activity / cadmium ion binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / rough endoplasmic reticulum / inclusion body / ERK1 and ERK2 cascade / cellular response to copper ion / cellular response to cadmium ion / activation of protein kinase B activity / removal of superoxide radicals / negative regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brain development / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cell growth / negative regulation of neurogenesis / synaptic vesicle / cellular response to oxidative stress / cellular response to hypoxia / response to oxidative stress / microtubule / negative regulation of neuron apoptotic process / mitochondrial outer membrane / dendritic spine / postsynaptic density / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / protein stabilization / ribosome / positive regulation of protein phosphorylation / copper ion binding / axon / negative regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular space / zinc ion binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING | ||||||
Model type details | minimized average | ||||||
Authors | Oz, G. / Zangger, K. / Armitage, I.M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Three-dimensional structure and dynamics of a brain specific growth inhibitory factor: metallothionein-3. Authors: Oz, G. / Zangger, K. / Armitage, I.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ji9.cif.gz | 18 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ji9.ent.gz | 13.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ji9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1ji9 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1ji9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3800.474 Da / Num. of mol.: 1 / Fragment: C-TERMINAL (ALPHA) DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / References: UniProt: P28184 |
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#2: Chemical | ChemComp-CD / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques and 2D 1H-113Cd HMQC spectroscopy. |
-Sample preparation
Details | Contents: 1.6 mM mouse metallothionein-3 / Solvent system: 20 mM deuterated Tris-HCl buffer | |||||||||||||||
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING Software ordinal: 1 Details: A total of 377 NOE-derived distance constraints and 16 cadmium-to-cysteine connectivities were used in the structure calculations. | ||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||
NMR ensemble | Conformer selection criteria: Minimized average structure / Conformers calculated total number: 50 / Conformers submitted total number: 1 |