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- SASDGB5: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bou... -

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Basic information

Entry
Database: SASBDB / ID: SASDGB5
SampleThe PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide
  • PDZ1-2 fragment of PSD-95/Disks large homolog 4 (protein), PDZ1-2, Homo sapiens
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / protein localization to synapse ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / protein localization to synapse / vocalization behavior / cerebellar mossy fiber / cellular response to potassium ion / Synaptic adhesion-like molecules / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / juxtaparanode region of axon / negative regulation of receptor internalization / neuron projection terminus / postsynaptic neurotransmitter receptor diffusion trapping / acetylcholine receptor binding / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / regulation of NMDA receptor activity / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Signaling by ERBB4 / 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 / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / Long-term potentiation / positive regulation of protein tyrosine kinase activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / D1 dopamine receptor binding / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / 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 / cell junction / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / scaffold protein binding / protein-containing complex assembly / basolateral plasma membrane / protein phosphatase binding / 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 / cytosol / cytoplasm
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationDate: 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
  • Stephen Prince (University of Manchester, Manchester, UK)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #3709
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3710
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3711
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3712
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3713
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3714
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3715
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3716
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3717
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #3718
Type: atomic / Chi-square value: 8.74
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide
Specimen concentration: 15 mg/ml
BufferName: 20 mM TRIS/HCl, 150 mM NaCl + 10 mM RRESEI / pH: 8.5 / Comment: standard buffer plus 10mM ligand peptide
Entity #1889Name: 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

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Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.123987 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 2M
Scan
Title: The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide
Measurement date: Jun 11, 2015 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 0.05 sec. / Number of frames: 15 / Unit: 1/A /
MinMax
Q0.0085 0.4799
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 726 /
MinMax
Q0.024096 0.215648
P(R) point1 726
R0 131
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; 0.112. 2; 1; 21; EOM; 0.186. 3; 1; 21; EOM; 0.656. 4; 2; 42; clustering Spacegroup; 0.000. 5; 4; 84; clustering Spacegroup; 0.000. 6; 8; 168; clustering Spacegroup; 0.034. 7; 12, 252; clustering Spacegroup; 0.005. 8; 16, 336, clustering Spacegroup; 0.000. 9; 20, 420, clustering Spacegroup; 0.000. 10; 24, 504, clustering Spacegroup; 0.006.
ExperimentalPorod
MW20.8 kDa20 kDa
Volume-32 nm3

P(R)GuinierGuinier error
Forward scattering, I048010 47587.5 86.36
Radius of gyration, Rg3.12 nm2.969 nm1.54

MinMax
D-13.1
Guinier point60 98

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