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Yorodumi- PDB-6qji: Crystal Structure of the third PDZ domain of PSD-95 protein: spac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qji | |||||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 | |||||||||
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 / 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 / Signaling by ERBB4 / 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 / 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 / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cell junction / endocytic vesicle membrane / synaptic vesicle / nervous system development / RAF/MAP kinase cascade / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein phosphatase binding / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / signal transduction / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 | 6qji.cif.gz | 317.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qji.ent.gz | 267.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qji_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 6qji_full_validation.pdf.gz | 479.3 KB | Display | |
Data in XML | 6qji_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 6qji_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/6qji ftp://data.pdbj.org/pub/pdb/validation_reports/qj/6qji | HTTPS FTP |
-Related structure data
Related structure data | 6qjdC 6qjfC 6qjgC 6qjjC 6qjkC 6qjlC 6qjnC 3k82S 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10660.919 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352 #2: Chemical | ChemComp-SO4 / #3: 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 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→19.97 Å / Num. obs: 80715 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 16.6 / Num. measured all: 618089 / Scaling rejects: 133 | ||||||||||||||||||||||||||||||
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: 3K82 Resolution: 1.5→19.972 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 26.11 / 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: 69.42 Å2 / Biso mean: 23.5923 Å2 / Biso min: 6.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.972 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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