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Yorodumi- PDB-1y7n: Solution structure of the second PDZ domain of the human neuronal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7n | ||||||
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Title | Solution structure of the second PDZ domain of the human neuronal adaptor X11alpha | ||||||
Components | Amyloid beta A4 precursor protein-binding family A member 1 | ||||||
Keywords | PROTEIN TRANSPORT / copper chaperone for superoxide dismutase / neuronal adaptor | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / synaptic vesicle / nervous system development / amyloid-beta binding / regulation of gene expression / protein-containing complex assembly / chemical synaptic transmission / in utero embryonic development / dendritic spine / cell adhesion / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance, dihedral angle restraints | ||||||
Authors | Duquesne, A.E. / de Ruijter, M. / Brouwer, J. / Drijfhout, J.W. / Nabuurs, S.B. / Spronk, C.A.E.M. / Vuister, G.W. / Ubbink, M. / Canters, G.W. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2005 Title: Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase Authors: Duquesne, A.E. / de Ruijter, M. / Brouwer, J. / Drijfhout, J.W. / Nabuurs, S.B. / Spronk, C.A.E.M. / Vuister, G.W. / Ubbink, M. / Canters, G.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y7n.cif.gz | 510.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7n.ent.gz | 429.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y7n_validation.pdf.gz | 339.9 KB | Display | wwPDB validaton report |
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Full document | 1y7n_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 1y7n_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1y7n_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7n ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7n | HTTPS FTP |
-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 | Mass: 9933.563 Da / Num. of mol.: 1 / Fragment: second PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: APBA1 / Plasmid: pET3H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) *RP / References: UniProt: Q02410 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2mM PDZ2a U-15N,13C; 10mM sodium phosphate buffer; pH 6.7; 95% H2O; 5% D2O Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 10mM / pH: 6.7 / Pressure: 1 atm / Temperature: 290 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance, dihedral angle restraints Software ordinal: 1 Details: The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the ...Details: The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the DYANA torsion angle dynamics algorithm. Using the FormatConverter, developed as part of the Collaborative Computing Project for the NMR Community (CCPN), the distance and dihedral angle restraints were converted to the X-PLOR restraint format. Subsequently the 100 generated structures were refined using a sh rt restrained molecular dynamics simulation in explicit solvent in the program XPLOR-NIH. Of these, the 20 lowest energy structures were selected to form the final ensemble. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |