+Open data
-Basic information
Entry | Database: PDB / ID: 3k82 | |||||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 | |||||||||
Components | Disks large homolog 4 | |||||||||
Keywords | CELL ADHESION / alpha and beta protein / Cell junction / Cell membrane / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse | |||||||||
Function / homology | Function and homology information LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / Synaptic adhesion-like molecules / cellular response to potassium ion / protein localization to synapse / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / acetylcholine receptor binding / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / cortical cytoskeleton / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / Long-term potentiation / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / D1 dopamine 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 / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / synaptic membrane / learning / PDZ domain binding / postsynaptic density membrane / adherens junction / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / kinase binding / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum / signal transduction / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | |||||||||
Authors | Camara-Artigas, A. / Gavira, J.A. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Novel conformational aspects of the third PDZ domain of the neuronal post-synaptic density-95 protein revealed from two 1.4A X-ray structures Authors: Camara-Artigas, A. / Murciano-Calles, J. / Gavira, J.A. / Cobos, E.S. / Martinez, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k82.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k82.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/3k82 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/3k82 | HTTPS FTP |
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-Related structure data
Related structure data | 3i4wC 1bfeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10512.738 Da / Num. of mol.: 1 / Fragment: Third PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78352 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-EPE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES sodium pH 7.5, 0.8M sodium phosphate monobasic monohydrate, 0.8M potassium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.993 Å / Num. all: 16937 / Num. obs: 16934 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 13.076 Å2 / Rmerge(I) obs: 0.0548 / Rsym value: 0.0548 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.3079 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3139 / Rsym value: 0.3079 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BFE Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.875 / SU B: 1.026 / SU ML: 0.042 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.48 Å2 / Biso mean: 17.095 Å2 / Biso min: 3.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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