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- PDB-6qjj: Crystal Structure of the third PDZ domain of PSD-95 protein: spac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qjj | |||||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3221 | |||||||||
![]() | Disks large homolog 4 | |||||||||
![]() | SIGNALING PROTEIN / pdz domain | |||||||||
Function / homology | ![]() LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / Synaptic adhesion-like molecules / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / regulation of NMDA receptor activity / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Signaling by ERBB4 / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / Long-term potentiation / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / learning / synaptic membrane / PDZ domain binding / adherens junction / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / kinase binding / cell-cell adhesion / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / signal transduction / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Camara-Artigas, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95. Authors: Camara-Artigas, A. / Murciano-Calles, J. / Martinez, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.3 KB | Display | ![]() |
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PDB format | ![]() | 46.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qjdC ![]() 6qjfC ![]() 6qjgC ![]() 6qjiC ![]() 6qjkC ![]() 6qjlC ![]() 6qjnC ![]() 3k82S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10660.919 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.17 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2015 | ||||||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.7→18.95 Å / Num. obs: 16133 / % possible obs: 99.7 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Rrim(I) all: 0.058 / Net I/σ(I): 22.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K82 Resolution: 1.7→18.945 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 34.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.24 Å2 / Biso mean: 59.7322 Å2 / Biso min: 28.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→18.945 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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