+Open data
-Basic information
Entry | Database: PDB / ID: 2f3n | ||||||
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Title | Crystal Structure of the native Shank SAM domain. | ||||||
Components | SH3 and multiple ankyrin repeat domains 3 | ||||||
Keywords | STRUCTURAL PROTEIN / Postsynaptic density / SAM domain / shank / scaffolding protein | ||||||
Function / homology | Function and homology information response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation / Neurexins and neuroligins / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly / vocal learning / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / structural constituent of postsynaptic density / regulation of grooming behavior / NMDA glutamate receptor clustering / vocalization behavior / regulation of dendritic spine morphogenesis / regulation of behavioral fear response / neuron spine / AMPA glutamate receptor clustering / neural precursor cell proliferation / locomotion / dendritic spine morphogenesis / brain morphogenesis / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / regulation of postsynapse organization / ciliary membrane / exploration behavior / regulation of long-term synaptic depression / adult behavior / positive regulation of dendritic spine development / locomotory exploration behavior / postsynaptic density, intracellular component / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / glial cell proliferation / synapse assembly / ionotropic glutamate receptor binding / positive regulation of synaptic transmission, glutamatergic / locomotory behavior / learning / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / G protein-coupled receptor binding / regulation of synaptic plasticity / modulation of chemical synaptic transmission / memory / SH3 domain binding / : / MAPK cascade / gene expression / actin binding / scaffold protein binding / dendritic spine / postsynaptic density / learning or memory / neuron projection / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, MAD / Resolution: 2.1 Å | ||||||
Authors | Baron, M.K. / Bowie, J.U. / Faham, S. | ||||||
Citation | Journal: Science / Year: 2006 Title: An architectural framework that may lie at the core of the postsynaptic density. Authors: Baron, M.K. / Boeckers, T.M. / Vaida, B. / Faham, S. / Gingery, M. / Sawaya, M.R. / Salyer, D. / Gundelfinger, E.D. / Bowie, J.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f3n.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f3n.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f3n ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f3n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9092.104 Da / Num. of mol.: 3 / Fragment: SAM Domain / Mutation: M55E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank3 / Plasmid: Pet3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JLU4 #2: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Well solution: 0.1 M HEPES pH 7.2, 0.4M Ammonium Formate, 6.5 mM N-nonyl BD Glucoside. Protein Buffer: 5mM tris pH 8.0, 50 mM NaCl, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277.K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 14919 / Num. obs: 14919 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 9.6 / Rsym value: 0.364 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIR, MAD / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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