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Yorodumi- PDB-1rgr: Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rgr | ||||||
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Title | Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DE NOVO PROTEIN / PDZ1 domain / STRUCTURAL PROTEIN-DE NOVO PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / proximal dendrite / AMPA glutamate receptor clustering / cerebellar mossy fiber / protein localization to synapse / cellular response to potassium ion / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / dendritic branch / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / neuron projection terminus / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / frizzled binding / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / regulation of neuronal synaptic plasticity / locomotory exploration behavior / cortical cytoskeleton / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / kinesin binding / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynaptic membrane / postsynapse / scaffold protein binding / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, cartesian MD in water | ||||||
Authors | Piserchio, A. / Salinas, G.D. / Li, T. / Marshall, J. / Spaller, M.R. / Mierke, D.F. | ||||||
Citation | Journal: Chem.Biol. / Year: 2004 Title: Targeting Specific PDZ Domains of PSD-95; Structural Basis for Enhanced Affinity and Enzymatic Stability of a Cyclic Peptide. Authors: Piserchio, A. / Salinas, G.D. / Li, T. / Marshall, J. / Spaller, M.R. / Mierke, D.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rgr.cif.gz | 654.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rgr.ent.gz | 566.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/1rgr ftp://data.pdbj.org/pub/pdb/validation_reports/rg/1rgr | 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 | Mass: 10860.138 Da / Num. of mol.: 1 / Fragment: PDZ1 domain of PSD-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DLG4, PSD95 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016 |
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#2: Protein/peptide | Mass: 768.897 Da / Num. of mol.: 1 / Fragment: C-terminus / Mutation: Q98K, S100E / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: GenBank: 3098551 |
#3: Chemical | ChemComp-BAL / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Contents: 1mM PZ1 U-15N,13C, 3mM peptide, 10 mM phospate buffer 150 mM NaCl, pH 6.8 Solvent system: 90% H2O/10% D2O |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, cartesian MD in water / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 22 |