+Open data
-Basic information
Entry | Database: PDB / ID: 1bfe | ||||||
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Title | THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 | ||||||
Components | PSD-95DLG4 | ||||||
Keywords | PEPTIDE RECOGNITION / PROTEIN LOCALIZATION | ||||||
Function / homology | Function and homology information RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / proximal dendrite / AMPA glutamate receptor clustering / cerebellar mossy fiber / protein localization to synapse / cellular response to potassium ion / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / dendritic branch / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / neuron projection terminus / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / frizzled binding / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / regulation of neuronal synaptic plasticity / locomotory exploration behavior / cortical cytoskeleton / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / kinesin binding / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynaptic membrane / postsynapse / scaffold protein binding / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / Mackinnon, R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Authors: Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / MacKinnon, R. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal Structure of the Hcask Pdz Domain Reveals Structural Basis of Class II Pdz Domain Target Recognition Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T. #2: Journal: Nature / Year: 1996 Title: Crystal Structure of a Pdz Domain Authors: Cabral, M. / Petosa, C. / Sutcliffe, M.J. / Raza, S. / Byron, O. / Poy, F. / Marfatia, S.M. / Chishti, A.H. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bfe.cif.gz | 34.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bfe.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/1bfe ftp://data.pdbj.org/pub/pdb/validation_reports/bf/1bfe | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12750.126 Da / Num. of mol.: 1 / Fragment: THE THIRD PDZ DOMAIN OF PSD-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P31016 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.95 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 0.8 M SODIUM CITRATE, 0.1 M HEPES, PH 7.5 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 6421 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.166 / % possible all: 86.7 |
Reflection | *PLUS Num. measured all: 38267 |
Reflection shell | *PLUS % possible obs: 90.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→20 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.214 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Rfactor obs: 0.214 / Rfactor Rfree: 0.315 / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Num. reflection obs: 5322 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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