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Yorodumi- PDB-2qs2: Crystal structure of the GluR5 ligand binding core dimer in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qs2 | ||||||
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Title | Crystal structure of the GluR5 ligand binding core dimer in complex with UBP318 at 1.80 Angstroms resolution | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Phosphorylation / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport | ||||||
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 / modulation of excitatory postsynaptic potential / behavioral response to pain / 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 / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / nervous system development / chemical synaptic transmission / scaffold protein binding / postsynaptic density / receptor complex / neuronal cell body / dendrite / synapse / glutamatergic synapse / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Alushin, G.M. / Jane, D.E. / Mayer, M.L. | ||||||
Citation | Journal: Neuropharmacology / Year: 2011 Title: Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists. Authors: Alushin, G.M. / Jane, D. / Mayer, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qs2.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qs2.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 2qs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/2qs2 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/2qs2 | HTTPS FTP |
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-Related structure data
Related structure data | 2qs1C 2qs4C 2f34S 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Details | The symmetry operator to build the biological dimer for chain A is x,-y,-z |
-Components
#1: Protein | Mass: 29211.531 Da / Num. of mol.: 2 / Mutation: E258S Source method: isolated from a genetically manipulated source Details: Residues 1-2 are a cloning artefact. Residues 3-116 and 119-258 correspond to P 22756 residues 446-559 and 682-821, and are linked by residues 117-118. Residue 258 is engineered. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET22b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P22756 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 21% PEG 1K, 100mM Tris-Cl, 2.5mM UBP318, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.91915 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2006 |
Radiation | Monochromator: Double Crystal Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91915 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 58102 / Num. obs: 58102 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 23.05 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 5.22 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2F34 Resolution: 1.8→32.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.203 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.124 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.225 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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