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Yorodumi- PDB-1jxm: CRYSTAL STRUCTURE OF THE GMP BOUND SH3-HOOK-GK FRAGMENT OF PSD-95 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jxm | ||||||
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Title | CRYSTAL STRUCTURE OF THE GMP BOUND SH3-HOOK-GK FRAGMENT OF PSD-95 | ||||||
Components | POSTSYNAPTIC DENSITY PROTEIN | ||||||
Keywords | STRUCTURAL PROTEIN / MAGUK / postsynaptic density / SH3 domain / guanylate kinase domain | ||||||
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 / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Tavares, G.A. / Panepucci, E.H. / Brunger, A.T. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structural characterization of the intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95. Authors: Tavares, G.A. / Panepucci, E.H. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxm.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxm.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxm ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxm | 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
#1: Protein | Mass: 34812.996 Da / Num. of mol.: 1 / Fragment: SH3-HOOK-GK Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PSD-95 / Organ: BRAIN / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3* / References: UniProt: P31016 | ||||
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#2: Chemical | ChemComp-5GP / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 2-methyl-2,4-pentanediol, HEPES buffer, guanidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→22.72 Å / Num. all: 26060 / Num. obs: 25218 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.042 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7 % / Num. unique all: 1263 / Rsym value: 0.135 / % possible all: 98.8 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 26060 / % possible obs: 97.5 % / Rmerge(I) obs: 0.042 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.135 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→22.72 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2161953.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.4218 Å2 / ksol: 0.405815 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.285 / % reflection Rfree: 10 % / Rfactor Rwork: 0.245 |