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Yorodumi- PDB-3u92: Crystal structure of the GluK3 ligand binding domain complex with... -
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-Basic information
Entry | Database: PDB / ID: 3u92 | ||||||
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Title | Crystal structure of the GluK3 ligand binding domain complex with kainate and zinc: P2221 form | ||||||
Components | Glutamate receptor, ionotropic kainate 3 | ||||||
Keywords | MEMBRANE PROTEIN / ION CHANNEL | ||||||
Function / homology | Function and homology information Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kumar, J. / Mayer, M.L. | ||||||
Citation | Journal: Neuron / Year: 2012 Title: Zinc Potentiates GluK3 Glutamate Receptor Function by Stabilizing the Ligand Binding Domain Dimer Interface. Authors: Veran, J. / Kumar, J. / Pinheiro, P.S. / Athane, A. / Mayer, M.L. / Perrais, D. / Mulle, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u92.cif.gz | 312.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u92.ent.gz | 258.7 KB | Display | PDB format |
PDBx/mmJSON format | 3u92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u92_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 3u92_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 3u92_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 3u92_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u92 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u92 | HTTPS FTP |
-Related structure data
Related structure data | 3u93C 3u94C 1s50S C: citing same article (ref.) 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 on special symmetry positions |
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Details | THE OBSERVED BIOLOGICAL UNIT DOES NOT OCCUR FOR THE FULL LENGTH PROTEIN THEREFORE, IS NOT BIOLOGICALLY RELEVANT |
-Components
#1: Protein | Mass: 29053.371 Da / Num. of mol.: 2 / Fragment: unp residues 433-546 and 669-807 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK3 / Plasmid: PET22 modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P42264 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZ | |
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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: 2.79 Å3/Da / Density % sol: 55.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 5% PEG 8K, 0.1 M Tris, 4 mM Kainate, 2 mM ZnAcetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45 Å / Num. all: 52357 / Num. obs: 52357 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.9 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S50 Resolution: 1.9→42.53 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.585 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→42.53 Å
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Refine LS restraints |
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LS refinement shell |
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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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