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Yorodumi- PDB-1ycj: Crystal structure of the kainate receptor GluR5 ligand-binding co... -
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-Basic information
Entry | Database: PDB / ID: 1ycj | ||||||
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Title | Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate | ||||||
Components | Ionotropic glutamate receptor 5 | ||||||
Keywords | MEMBRANE PROTEIN / Ionotropic glutamate receptor / Kainate receptor / GluR5 ligand-binding core | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: Febs Lett. / Year: 2005 Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ycj.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ycj.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ycj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ycj_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 1ycj_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 1ycj_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 1ycj_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycj ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycj | HTTPS FTP |
-Related structure data
Related structure data | 1ftjS 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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Details | The two protomers in the asymmetric unit constitutes a dimer of the tetrameric multimer representing the known biologically significant oligomerization state of the functional ion channel. |
-Components
#1: Protein | Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: GluR5 ligand-binding core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756, GenBank: 204390 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG4000, phosphat-citrate buffer, lithiumsulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8128 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8128 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→25 Å / Num. all: 37489 / Num. obs: 37372 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.94→2.01 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 3721 / Rsym value: 0.314 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FTJ Resolution: 1.95→20.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.787 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.497 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.947→1.997 Å / Total num. of bins used: 20
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