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Yorodumi- PDB-5mz7: Crystal Structure of the third PDZ domain from the synaptic prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mz7 | |||||||||
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Title | Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine | |||||||||
Components | Disks large homolog 4 | |||||||||
Keywords | PEPTIDE BINDING PROTEIN / Azidohomoalanine / Non-standard amino acid / unnatural amino acid / artificial amino acid / PSD-95 | |||||||||
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 / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse ...RHO GTPases activate CIT / 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 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 / 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 / postsynapse / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / synapse / glutamatergic 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 / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
Authors | Kudlinzki, D. / Lehner, F. / Witt, K. / Linhard, V.L. / Silvers, R. / Schwalbe, H. | |||||||||
Citation | Journal: Chembiochem / Year: 2017 Title: Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding. Authors: Lehner, F. / Kudlinzki, D. / Richter, C. / Muller-Werkmeister, H.M. / Eberl, K.B. / Bredenbeck, J. / Schwalbe, H. / Silvers, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mz7.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mz7.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/5mz7 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/5mz7 | HTTPS FTP |
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-Related structure data
Related structure data | 5w72C 1bfeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10802.950 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: P31016 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.1 M sodium citrate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→47.09 Å / Num. obs: 54545 / % possible obs: 97.6 % / Observed criterion σ(I): 2.1 / Redundancy: 2.3 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.53→1.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.831 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BFE Resolution: 1.53→47.086 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→47.086 Å
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Refine LS restraints |
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LS refinement shell |
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