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- PDB-1kef: PDZ1 of SAP90 -

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Basic information

Entry
Database: PDB / ID: 1kef
TitlePDZ1 of SAP90
Componentssynapse associated protein-90
KeywordsPROTEIN BINDING / beta-sheet / anti-parallel beta-sandwich / GLGF loop
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 / embryo development / receptor localization to synapse ...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 / embryo development / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / Synaptic adhesion-like molecules / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / juxtaparanode region of axon / negative regulation of receptor internalization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / Neurexins and neuroligins / regulation of NMDA receptor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Signaling by ERBB4 / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / positive regulation of excitatory postsynaptic potential / social behavior / 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 / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / learning / synaptic membrane / PDZ domain binding / adherens junction / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / 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 / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm / cytosol
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. / Guanylate kinase-like domain ...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 / Pdz3 Domain / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing with torsion angle restraints
AuthorsPiserchio, A. / Pellegrini, M. / Mehta, S. / Blackman, S.M. / Garcia, E.P. / Marshall, J. / Mierke, D.F.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The PDZ1 domain of SAP90. Characterization of structure and binding.
Authors: Piserchio, A. / Pellegrini, M. / Mehta, S. / Blackman, S.M. / Garcia, E.P. / Marshall, J. / Mierke, D.F.
History
DepositionNov 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: synapse associated protein-90


Theoretical massNumber of molelcules
Total (without water)10,0311
Polymers10,0311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100average structure from ensemble of 28 structures, chosen by energy and penalty function
RepresentativeModel #1closest to the average

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Components

#1: Protein synapse associated protein-90 / (SAP90) / presynaptic density protein 95 / PSD-95


Mass: 10031.256 Da / Num. of mol.: 1 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P78352

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 1.0 mM protein, 10 mM phosphate buffer, 150 mM NaCl, pH 6.8
Solvent system: 10 mM phosphate buffer, 150 mM NaCl
Sample conditionsIonic strength: 150 mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio F.data analysis
X-PLORCNSBruenger, A.refinement
RefinementMethod: simulated annealing with torsion angle restraints / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: average structure from ensemble of 28 structures, chosen by energy and penalty function
Conformers calculated total number: 100 / Conformers submitted total number: 1

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