+Open data
-Basic information
Entry | Database: PDB / ID: 2ka9 | ||||||
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Title | Solution structure of PSD-95 PDZ12 complexed with cypin peptide | ||||||
Components |
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Keywords | CELL ADHESION / PDZ-cypin peptide complex / tandem PDZ domain / Alternative splicing / Cell junction / Cell membrane / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse | ||||||
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 / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / frizzled binding / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / 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 / cortical cytoskeleton / regulation of neuronal synaptic plasticity / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / kinesin binding / AMPA glutamate receptor complex / 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 / postsynapse / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / synapse / glutamatergic 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 / simulated annealing | ||||||
Authors | Wang, W.N. / Weng, J.W. / Zhang, X. / Liu, M.L. / Zhang, M.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Creating conformational entropy by increasing interdomain mobility in ligand binding regulation: a revisit to N-terminal tandem PDZ domains of PSD-95 Authors: Wang, W.N. / Weng, J.W. / Zhang, X. / Liu, M.L. / Zhang, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ka9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ka9.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2ka9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/2ka9 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/2ka9 | 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: 20126.957 Da / Num. of mol.: 1 / Fragment: N-terminal PDZ12 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31016 |
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#2: Protein/peptide | Mass: 949.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 15N-separated NOESY |
-Sample preparation
Details | Contents: 1mM [U-15N] PSD95 PDZ12, 1mM cypin peptide, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CNS / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: This structure is not superimposed because the relative domain orientation is not defined due to its intrinsic conformational flexibility. |
NMR constraints | NOE constraints total: 3564 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |
NMR ensemble rms | Bond angle rms dev: 0.393 ° / Covalent bond rms dev: 0.0021 Å / Dihedral angles rms dev: 29.297 ° / Improper torsion angle rms dev: 0.287 ° |