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- PDB-5j7j: NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j7j | |||||||||
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Title | NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95 | |||||||||
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![]() | METAL BINDING PROTEIN / phosphorylated / calmodulin / PSD-95 / Voltage-Gated Channel | |||||||||
Function / homology | ![]() LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / cellular response to potassium ion ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / cellular response to potassium ion / vocalization behavior / cerebellar mossy fiber / neuron spine / Synaptic adhesion-like molecules / AMPA glutamate receptor clustering / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / Trafficking of AMPA receptors / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / myosin II complex / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Long-term potentiation / Signaling by ERBB4 / neuromuscular process controlling balance / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / PDZ domain binding / learning / adherens junction / synaptic membrane / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / cell-cell adhesion / neuromuscular junction / kinase binding / endocytic vesicle membrane / cell junction / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / signaling receptor binding / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
![]() | Turner, M.L. / Ames, J.B. / Anderson, D.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ca2+/calmodulin binding to PSD-95 mediates homeostatic synaptic scaling down. Authors: Chowdhury, D. / Turner, M. / Patriarchi, T. / Hergarden, A.C. / Anderson, D. / Zhang, Y. / Sun, J. / Chen, C.Y. / Ames, J.B. / Hell, J.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.3 KB | Display | ![]() |
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PDB format | ![]() | 168.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 456.9 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Xenopus laevis Calmodulin / Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 2408.641 Da / Num. of mol.: 1 / Fragment: UNP residues 1-19 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: Chemical | ChemComp-CA / Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O Details: 15N, 13C labeled Calmodlin Bound to unlabeled PSD-95 Label: 15N,13C Calmodulin / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Details: 20mM d-11 Tris pH 7.0, 5mM CaCl2, 50mM NaCl, 8% D2O Ionic strength: 50 mM / Label: CaM Buffer / pH: 7 / Pressure: 1 atm / Temperature: 318 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 4 |