+Open data
-Basic information
Entry | Database: PDB / ID: 2awx | ||||||
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Title | Synapse associated protein 97 PDZ2 domain variant C378S | ||||||
Components | Synapse associated protein 97 | ||||||
Keywords | MEMBRANE PROTEIN / synaptic signaling / trafficking protein | ||||||
Function / homology | Function and homology information tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization ...tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / cell projection membrane / paranode region of axon / smooth muscle tissue development / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / Activation of Ca-permeable Kainate Receptor / regulation of ventricular cardiac muscle cell action potential / amyloid precursor protein metabolic process / node of Ranvier / establishment or maintenance of epithelial cell apical/basal polarity / protein-containing complex localization / endothelial cell proliferation / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / ureteric bud development / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / postsynaptic density, intracellular component / microvillus / kinesin binding / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / potassium channel regulator activity / lateral plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of T cell proliferation / ionotropic glutamate receptor binding / T-tubule / actin filament polymerization / regulation of membrane potential / T cell activation / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / PDZ domain binding / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / neuromuscular junction / protein localization / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / synaptic vesicle membrane / cell-cell adhesion / cerebral cortex development / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / presynaptic membrane / cell junction / regulation of cell shape / chemical synaptic transmission / postsynaptic membrane / basolateral plasma membrane / cell population proliferation / microtubule / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / cell adhesion / neuron projection / membrane raft / apical plasma membrane / dendrite / neuronal cell body / glutamatergic synapse / synapse / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Von Ossowski, I. / Oksanen, E. / Von Ossowski, L. / Cai, C. / Sundberg, M. / Goldman, A. / Keinanen, K. | ||||||
Citation | Journal: Febs J. / Year: 2006 Title: Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptide Authors: von Ossowski, I. / Oksanen, E. / von Ossowski, L. / Cai, C. / Sundberg, M. / Goldman, A. / Keinanen, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2awx.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2awx.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 2awx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/2awx ftp://data.pdbj.org/pub/pdb/validation_reports/aw/2awx | HTTPS FTP |
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-Related structure data
Related structure data | 2awuC 2awwC 2g2lC 1yuq C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11455.189 Da / Num. of mol.: 2 / Fragment: PDZ2 domain / Mutation: C378S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg1 / Plasmid: PK0302-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q62696 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THIS CONFLICT IS ESTABILISHED ERRORS IN THE SEQUENCE DATABASE. THE AUTHOR BELIEVE THAT THESE ...THIS CONFLICT IS ESTABILISH | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2005 |
Radiation | Monochromator: Diamond (111), germanium (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 38640 / Num. obs: 38640 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.49 |
Reflection shell | Resolution: 1.8→1.91 Å / % possible obs: 89.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.04 / Num. measured obs: 5857 / Num. unique obs: 2339 / % possible all: 97.3 |
-Phasing
Phasing MR | Rfactor: 0.468 / Cor.coef. Fo:Fc: 0.436
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.329 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.909 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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