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Yorodumi- PDB-4x3i: The crystal structure of Arc N-lobe complexed with CAMK2A fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x3i | ||||||
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Title | The crystal structure of Arc N-lobe complexed with CAMK2A fragment | ||||||
Components |
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Keywords | SIGNALING PROTEIN / ENDOCYTOSIS MEDIATOR | ||||||
Function / homology | Function and homology information regulation of synaptic vesicle docking / glutamatergic postsynaptic density / postsynaptic endosome / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / vesicle-mediated intercellular transport / Unblocking of NMDA receptors, glutamate binding and activation / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway ...regulation of synaptic vesicle docking / glutamatergic postsynaptic density / postsynaptic endosome / HSF1-dependent transactivation / Interferon gamma signaling / Ion transport by P-type ATPases / vesicle-mediated intercellular transport / Unblocking of NMDA receptors, glutamate binding and activation / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / Trafficking of AMPA receptors / calcium- and calmodulin-dependent protein kinase complex / RAF activation / neuronal ribonucleoprotein granule / calmodulin dependent kinase signaling pathway / Ca2+ pathway / RAF/MAP kinase cascade / calcium-dependent protein serine/threonine kinase activity / NMDA selective glutamate receptor signaling pathway / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / clathrin-coated vesicle membrane / regulation of neurotransmitter secretion / dendritic spine development / endoderm development / regulation of dendritic spine morphogenesis / Ion homeostasis / positive regulation of calcium ion transport / postsynaptic neurotransmitter receptor diffusion trapping / response to morphine / postsynaptic specialization membrane / presynaptic cytosol / negative regulation of hydrolase activity / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / calmodulin-dependent protein kinase activity / regulation of long-term synaptic potentiation / GTPase activating protein binding / dendrite morphogenesis / positive regulation of AMPA receptor activity / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / anterior/posterior pattern specification / postsynaptic cytosol / regulation of long-term synaptic depression / regulation of neuronal synaptic plasticity / positive regulation of cardiac muscle cell apoptotic process / mRNA transport / long-term memory / glutamate receptor binding / cellular response to interferon-beta / regulation of protein localization to plasma membrane / cytoskeleton organization / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / acrosomal vesicle / learning / response to ischemia / angiotensin-activated signaling pathway / postsynaptic density membrane / G1/S transition of mitotic cell cycle / positive regulation of receptor signaling pathway via JAK-STAT / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / protein homooligomerization / cellular response to type II interferon / endocytosis / extracellular vesicle / calcium ion transport / cell migration / actin cytoskeleton / cell cortex / kinase activity / early endosome membrane / peptidyl-serine phosphorylation / dendritic spine / postsynaptic density / calmodulin binding / neuron projection / membrane raft / axon / protein serine kinase activity / mRNA binding / protein serine/threonine kinase activity / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhang, W. / Ward, M. / Leahy, D. / Worley, P. | ||||||
Citation | Journal: Neuron / Year: 2015 Title: Structural basis of arc binding to synaptic proteins: implications for cognitive disease. Authors: Zhang, W. / Wu, J. / Ward, M.D. / Yang, S. / Chuang, Y.A. / Xiao, M. / Li, R. / Leahy, D.J. / Worley, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x3i.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x3i.ent.gz | 20.2 KB | Display | PDB format |
PDBx/mmJSON format | 4x3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x3i ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3i | 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: 9393.229 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 207-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arc / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q63053 |
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#2: Protein/peptide | Mass: 752.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 309-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CAMK2A / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P11798*PLUS, Ca2+/calmodulin-dependent protein kinase |
#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: 2.82 Å3/Da / Density % sol: 56.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M AMMONIUM SULFATE AND 0.1 M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9801 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.763 Å / Num. obs: 9807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Net I/σ(I): 10.3 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→25.76 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.76 Å
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Refine LS restraints |
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LS refinement shell |
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