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Yorodumi- SASDGC5: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bou... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDGC5 |
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Sample | The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (diluted)
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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 / regulation of grooming behavior / synaptic vesicle maturation / receptor localization to synapse / cerebellar mossy fiber ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / Synaptic adhesion-like molecules / neuron spine / AMPA glutamate receptor clustering / juxtaparanode region of axon / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / neuron projection terminus / RHO GTPases activate CIT / postsynaptic neurotransmitter receptor diffusion trapping / Assembly and cell surface presentation of NMDA receptors / acetylcholine receptor binding / establishment or maintenance of epithelial cell apical/basal polarity / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of NMDA receptor activity / 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 / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / Long-term potentiation / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / positive regulation of synaptic transmission / extrinsic component of cytoplasmic side of plasma membrane / ionotropic glutamate receptor binding / 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 / 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 / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / protein-containing complex assembly / 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) |
Citation | Date: 2019 Sep 19 Title: How the dual PDZ domain from Postsynaptic density protein 95 clusters ion channels and receptors Authors: Rodzli N / Lockhart-Cairns M / Levy C / Chipperfield J / Bird L / Baldock C |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDGC5 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
-Sample
Sample | Name: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (diluted) Specimen concentration: 7.5 mg/ml |
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Buffer | Name: 20 mM TRIS/HCl, 150 mM NaCl + 5 mM RRESEI / pH: 8.5 |
Entity #1889 | Name: PDZ1-2 / Type: protein Description: PDZ1-2 fragment of PSD-95/Disks large homolog 4 Formula weight: 20.8 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P78352 Sequence: GPGTEGEMEY EEITLERGNS GLGFSIAGGT DNPHIGDDPS IFITKIIPGG AAAQDGRLRV NDSILFVNEV DVREVTHSAA VEALKEAGSI VRLYVMRRKP PAEKVMEIKL IKGPKGLGFS IAGGVGNQHI PGDNSIYVTK IIEGGAAHKD GRLQIGDKIL AVNSVGLEDV ...Sequence: GPGTEGEMEY EEITLERGNS GLGFSIAGGT DNPHIGDDPS IFITKIIPGG AAAQDGRLRV NDSILFVNEV DVREVTHSAA VEALKEAGSI VRLYVMRRKP PAEKVMEIKL IKGPKGLGFS IAGGVGNQHI PGDNSIYVTK IIEGGAAHKD GRLQIGDKIL AVNSVGLEDV MHEDAVAALK NTYDVVYLKV AKPSNA |
-Experimental information
Beam | Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.123987 Å / Dist. spec. to detc.: 3 mm | ||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 2M | ||||||||||||||||||||||||||||||
Scan | Title: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (diluted) Measurement date: Jun 11, 2015 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 0.05 sec. / Number of frames: 16 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 766 /
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Result | Type of curve: single_conc Comments: Scattering data are fitted using the ATSAS OLIGOMER program using a suite of models. The ATSAS program FFMAKER was used to generate form factors for each model in the suite. Each model is ...Comments: Scattering data are fitted using the ATSAS OLIGOMER program using a suite of models. The ATSAS program FFMAKER was used to generate form factors for each model in the suite. Each model is assigned a volume fraction to fit the observed scattering profile. 3 monomer models are included, the first is a compact conformation of PDZ1-2 similar to PDB entries 6spv/6spz; the other two are domain models obtained from a representative run of the ATSAS EOM program with data projected to infinite dilution. Multimeric models are drawn from a "clustering Spacegroup", unit cell 14.8nm symmetry I2(1)3, and consist of identical copies of an extended conformation of PDZ1-2 (similar to PDB entry 3zrt) assembled by symmetry operations. In the order of deposition: Model number; Stoichiometry; MW (kDa); source; Volume fraction. 1; 1; 21; Crystal Structure; 0.315. 2; 1; 21; EOM; 0.185. 3; 1; 21; EOM; 0.455. 4; 2; 42; clustering Spacegroup; 0.000. 5; 4; 84; clustering Spacegroup; 0.019. 6; 8; 168; clustering Spacegroup; 0.020. 7; 12, 252; clustering Spacegroup; 0.000. 8; 16, 336, clustering Spacegroup; 0.000. 9; 20, 420, clustering Spacegroup; 0.000. 10; 24, 504, clustering Spacegroup; 0.005.
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