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Yorodumi- PDB-6qjl: Crystal Structure of the third PDZ domain of PSD-95 protein D332G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qjl | |||||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P21 | |||||||||
Components | Disks large homolog 4 | |||||||||
Keywords | SIGNALING PROTEIN / pdz domain | |||||||||
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 / AMPA glutamate receptor clustering ...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 / AMPA glutamate receptor clustering / cerebellar mossy fiber / Synaptic adhesion-like molecules / protein localization to synapse / cellular response to potassium ion / vocalization behavior / neuron spine / juxtaparanode region of axon / neuron projection terminus / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / 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 / locomotory exploration behavior / cortical cytoskeleton / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / Long-term potentiation / 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 / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / 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 / chemical synaptic transmission / RAF/MAP kinase cascade / postsynaptic membrane / scaffold protein binding / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.043 Å | |||||||||
Authors | Camara-Artigas, A. | |||||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qjl.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qjl.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/6qjl ftp://data.pdbj.org/pub/pdb/validation_reports/qj/6qjl | HTTPS FTP |
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-Related structure data
Related structure data | 6qjdC 6qjfC 6qjgC 6qjiC 6qjjC 6qjkC 6qjnC 5oih S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11090.453 Da / Num. of mol.: 2 / Fragment: PDZ domain / Mutation: D332G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.01 % / Mosaicity: 0.28 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.17 M ammonium sulphate , 25.5% PEG 8000 , 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 / Details: sample-detector distance: adjustable 123-1356mm | ||||||||||||||||||||||||
Radiation | Monochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.04→47.02 Å / Num. obs: 153886 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 12 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OIH 5oih Resolution: 1.043→31.821 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 17.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.48 Å2 / Biso mean: 16.4975 Å2 / Biso min: 7.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.043→31.821 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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