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Yorodumi- PDB-7cqf: Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cqf | ||||||
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Title | Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide | ||||||
Components | Disks large homolog 4,Disintegrin and metalloproteinase domain-containing protein 22 | ||||||
Keywords | SIGNALING PROTEIN / Scaffold protein / Membrane receptor | ||||||
Function / homology | Function and homology information RHO GTPases activate CIT / LGI-ADAM interactions / 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 ...RHO GTPases activate CIT / LGI-ADAM interactions / 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 / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / frizzled binding / negative regulation of cell adhesion / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / 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 / cortical cytoskeleton / regulation of neuronal synaptic plasticity / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / kinesin binding / AMPA glutamate receptor complex / 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 / central nervous system development / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / metalloendopeptidase activity / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / integrin binding / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynapse / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / cell adhesion / neuron projection / axon / signaling receptor binding / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / proteolysis / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yamagata, A. / Fukai, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: LGI1-ADAM22-MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention. Authors: Fukata, Y. / Chen, X. / Chiken, S. / Hirano, Y. / Yamagata, A. / Inahashi, H. / Sanbo, M. / Sano, H. / Goto, T. / Hirabayashi, M. / Kornau, H.C. / Pruss, H. / Nambu, A. / Fukai, S. / Nicoll, R.A. / Fukata, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cqf.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cqf.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 7cqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/7cqf ftp://data.pdbj.org/pub/pdb/validation_reports/cq/7cqf | HTTPS FTP |
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-Related structure data
Related structure data | 1tp3S S: Starting model for refinement |
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Similar 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: 16446.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fusion protein of PSD-95 PDZ3, linker, and ADAM22 C-terminal peptide Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human) Gene: Dlg4, Dlgh4, Psd95, ADAM22, MDC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016, UniProt: Q9P0K1 | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | ChemComp-CHT / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M choline chloride, 0.1 M Tris-HCl (pH 7.5), 14 % (w/v) PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 10624 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.134 / Rsym value: 0.13 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 532 / CC1/2: 0.944 / Rpim(I) all: 0.262 / Rrim(I) all: 0.791 / Rsym value: 0.745 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TP3 Resolution: 1.8→36.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.781 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.53 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→36.64 Å
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