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Yorodumi- PDB-1yjr: Solution structure of the apo form of the sixth soluble domain A6... -
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-Basic information
Entry | Database: PDB / ID: 1yjr | ||||||
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Title | Solution structure of the apo form of the sixth soluble domain A69P mutant of Menkes protein | ||||||
Components | Copper-transporting ATPase 1 | ||||||
Keywords | HYDROLASE / metallochaperone / protein-protein interaction / copper(I) / metal homeostasis / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | Function and homology information peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation ...peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / cellular response to lead ion / pyramidal neuron development / copper ion export / copper ion import / copper ion homeostasis / copper ion transport / melanosome membrane / catecholamine metabolic process / serotonin metabolic process / detoxification of copper ion / norepinephrine metabolic process / trans-Golgi network transport vesicle / regulation of oxidative phosphorylation / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / response to manganese ion / negative regulation of iron ion transmembrane transport / cellular response to antibiotic / skin development / hair follicle morphogenesis / pigmentation / dopamine metabolic process / lung alveolus development / response to zinc ion / cellular response to platelet-derived growth factor stimulus / positive regulation of catalytic activity / cell leading edge / blood vessel development / central nervous system neuron development / Detoxification of Reactive Oxygen Species / cuprous ion binding / Ion transport by P-type ATPases / microvillus / positive regulation of cell size / intracellular copper ion homeostasis / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / lactation / removal of superoxide radicals / mitochondrion organization / extracellular matrix organization / neuron projection morphogenesis / trans-Golgi network membrane / liver development / secretory granule / locomotory behavior / positive regulation of epithelial cell proliferation / female pregnancy / cellular response to iron ion / brush border membrane / cellular response to amino acid stimulus / trans-Golgi network / small GTPase binding / phagocytic vesicle membrane / late endosome / early endosome membrane / protein-folding chaperone binding / cellular response to hypoxia / basolateral plasma membrane / perikaryon / in utero embryonic development / postsynaptic density / neuron projection / apical plasma membrane / copper ion binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing, restrained energy minimization | ||||||
Authors | Banci, L. / Bertini, I. / Cantini, F. / Migliardi, M. / Rosato, A. / Wang, S. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: An atomic-level investigation of the disease-causing A629P mutant of the Menkes protein, ATP7A Authors: Banci, L. / Bertini, I. / Cantini, F. / Migliardi, M. / Rosato, A. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yjr.cif.gz | 754.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjr.ent.gz | 643.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yjr_validation.pdf.gz | 355.6 KB | Display | wwPDB validaton report |
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Full document | 1yjr_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 1yjr_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 1yjr_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjr ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjr | HTTPS FTP |
-Related structure data
Related structure data | 1yjtC 1yjuC 1yjvC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8217.630 Da / Num. of mol.: 1 / Fragment: Sixth soluble domain / Mutation: A69P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q04656, Cu2+-exporting ATPase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing, restrained energy minimization Software ordinal: 1 Details: the structures were based on a total of 1947 meaningful distance constraints, 81 dihedral angle restraints | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30 |