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Yorodumi- PDB-1be9: THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 IN COMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1be9 | ||||||
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Title | THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 IN COMPLEX WITH A C-TERMINAL PEPTIDE DERIVED FROM CRIPT. | ||||||
Components |
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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 / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / frizzled binding / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / dendritic spine organization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / positive regulation of dendrite morphogenesis / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / cell junction / cell-cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein phosphatase binding / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER ANALYSIS / Resolution: 1.82 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 the Structural Basis of Class II Pdz Domain Target Recognition Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T. #2: Journal: Neuron / Year: 1998 Title: Cript, a Novel Postsynaptic Protein that Binds to the Third Pdz Domain of Psd-95/Sap90 Authors: Niethammer, M. / Valtschanoff, J.G. / Kapoor, T.M. / Allison, D.W. / Weinberg, T.M. / Craig, A.M. / Sheng, M. #3: 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 | 1be9.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1be9.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1be9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1be9_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 1be9_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 1be9_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1be9_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1be9 ftp://data.pdbj.org/pub/pdb/validation_reports/be/1be9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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: Protein/peptide | Mass: 562.636 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PEPTIDE / Source method: isolated from a natural source |
#3: 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: 2.23 Å3/Da / Density % sol: 44.87 % Description: THE PEPTIDE-FREE PDZ3 MODEL WAS USED IN A RIGID BODY REFINEMENT, FOLLOWED BY CYCLES OF LEAST-SQUARES REFINEMENT AND MODEL BUILDING. | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 0.8 M SODIUM CITRATE, 0.1 M HEPES, PH 7.5 | ||||||||||||||||||||||||
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: 1.82→20 Å / Num. obs: 11108 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.82→1.88 Å / Rmerge(I) obs: 0.144 / % possible all: 92.6 |
Reflection | *PLUS Num. measured all: 141652 |
Reflection shell | *PLUS % possible obs: 90.1 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER ANALYSIS / Resolution: 1.82→20 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.207 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 10737 / σ(F): 2 / Rfactor obs: 0.207 / Rfactor Rfree: 0.278 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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