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Yorodumi- PDB-5j7j: NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j7j | |||||||||
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Title | NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95 | |||||||||
Components |
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Keywords | METAL BINDING PROTEIN / phosphorylated / calmodulin / PSD-95 / Voltage-Gated Channel | |||||||||
Function / homology | Function and homology information LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / 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 / NrCAM interactions / 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 / Synaptic adhesion-like molecules / Signaling by ERBB4 / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / regulation of NMDA receptor activity / 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 / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / Long-term potentiation / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / positive regulation of synaptic transmission / enzyme regulator activity / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / learning / synaptic membrane / PDZ domain binding / adherens junction / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cell junction / endocytic vesicle membrane / synaptic vesicle / nervous system development / RAF/MAP kinase cascade / 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 / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / signal transduction / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Turner, M.L. / Ames, J.B. / Anderson, D.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Embo J. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j7j.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j7j.ent.gz | 173.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j7j_validation.pdf.gz | 421.9 KB | Display | wwPDB validaton report |
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Full document | 5j7j_full_validation.pdf.gz | 461 KB | Display | |
Data in XML | 5j7j_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 5j7j_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/5j7j ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j7j | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Xenopus laevis (African clawed frog) / Gene: calm1, calm2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS |
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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.) Homo sapiens (human) / References: UniProt: P78352 |
#3: Chemical | ChemComp-CA / |
-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 |