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- PDB-1zok: PDZ1 Domain Of Synapse Associated Protein 97 -

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Basic information

Entry
Database: PDB / ID: 1zok
TitlePDZ1 Domain Of Synapse Associated Protein 97
ComponentsPresynaptic protein SAP97
KeywordsMEMBRANE PROTEIN / PDZ / PDZ1 / SAP97 / Synapse Associated Protein 97 / Beta Strand / Helix
Function / homology
Function and homology information


tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / hard palate development / structural constituent of postsynaptic density ...tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / hard palate development / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / astral microtubule organization / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / epithelial structure maintenance / reproductive structure development / immunological synapse formation / lateral loop / receptor localization to synapse / myelin sheath abaxonal region / peristalsis / smooth muscle tissue development / bicellular tight junction assembly / cortical microtubule organization / cell projection membrane / paranode region of axon / Trafficking of AMPA receptors / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / Activation of Ca-permeable Kainate Receptor / regulation of ventricular cardiac muscle cell action potential / positive regulation of potassium ion transport / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / cortical actin cytoskeleton organization / lens development in camera-type eye / regulation of myelination / ureteric bud development / neurotransmitter receptor localization to postsynaptic specialization membrane / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / microvillus / kinesin binding / basement membrane / immunological synapse / Unblocking of NMDA receptors, glutamate binding and activation / bicellular tight junction / lateral plasma membrane / postsynaptic density, intracellular component / regulation of postsynaptic membrane neurotransmitter receptor levels / potassium channel regulator activity / phosphatase binding / T cell proliferation / ionotropic glutamate receptor binding / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of T cell proliferation / actin filament polymerization / T-tubule / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell activation / actin filament organization / basal plasma membrane / protein localization to plasma membrane / regulation of membrane potential / PDZ domain binding / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / neuromuscular junction / cerebral cortex development / cell-cell adhesion / cytoplasmic side of plasma membrane / kinase binding / synaptic vesicle membrane / negative regulation of epithelial cell proliferation / cell junction / intracellular protein localization / cell-cell junction / nervous system development / regulation of cell shape / regulation of protein localization / presynaptic membrane / basolateral plasma membrane / chemical synaptic transmission / molecular adaptor activity / microtubule / transmembrane transporter binding / postsynaptic membrane / cell population proliferation / neuron projection / postsynaptic density / cell adhesion
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWang, L. / Piserchio, A. / Mierke, D.F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Characterization of the Intermolecular Interactions of Synapse-associated Protein-97 with the NR2B Subunit of N-Methyl-D-aspartate Receptors.
Authors: Wang, L. / Piserchio, A. / Mierke, D.F.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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: Presynaptic protein SAP97


Theoretical massNumber of molelcules
Total (without water)10,0891
Polymers10,0891
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 / -structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Presynaptic protein SAP97 / Synapse-associated protein 97 / SAP-97 / Discs / large homolog 1


Mass: 10089.323 Da / Num. of mol.: 1 / Fragment: PDZ1 domain (residues 221-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q62696

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM C13-N15 PDZ1 of SAP97 in 20mM phosphate buffer, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: No salt / pH: 7.4 / Pressure: Normal air pressure / Temperature: 298 K

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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
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
NMRPipe2.3F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
XwinNMR3Bruker Biospincollection
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers submitted total number: 1

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