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- PDB-1um7: Solution structure of the third PDZ domain of synapse-associated ... -

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Entry
Database: PDB / ID: 1um7
TitleSolution structure of the third PDZ domain of synapse-associated protein 102
Componentssynapse-associated protein 102
KeywordsPROTEIN BINDING / PDZ / Discs large homolog 3 / DLG3-HUMAN presynaptic protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


establishment of planar polarity / NrCAM interactions / receptor localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission ...establishment of planar polarity / NrCAM interactions / receptor localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / Long-term potentiation / bicellular tight junction / phosphatase binding / positive regulation of protein tyrosine kinase activity / Ras activation upon Ca2+ influx through NMDA receptor / postsynaptic density membrane / adherens junction / neuromuscular junction / cell-cell adhesion / kinase binding / chemical synaptic transmission / RAF/MAP kinase cascade / basolateral plasma membrane / neuron projection / negative regulation of cell population proliferation / glutamatergic synapse / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol
Similarity search - Function
Disks Large homologue 3, SH3 domain / 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 ...Disks Large homologue 3, SH3 domain / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.-R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the third PDZ domain of synapse-associated protein 102
Authors: Qin, X.-R. / Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionSep 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: synapse-associated protein 102


Theoretical massNumber of molelcules
Total (without water)11,6551
Polymers11,6551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein synapse-associated protein 102 / KIAA1232 protein


Mass: 11654.825 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: Kazusa cDNA KIAA1232 / Plasmid: P021030-42 / References: UniProt: Q92796

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.05mM 13C, 15N-labeled protein; 20mM phosphate buffer; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Cvariancollection
NMRPipe20020425Delaglio. F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.854Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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