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Yorodumi- PDB-4u4g: Structure of GluA2* in complex with competitive antagonist ZK 200775 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u4g | |||||||||
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Title | Structure of GluA2* in complex with competitive antagonist ZK 200775 | |||||||||
Components | Glutamate receptor 2GRIA2 | |||||||||
Keywords | TRANSPORT PROTEIN / Ionotropic glutamate receptor / AMPA receptor / competitive antagonist / tetramer / complex | |||||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / chemical synaptic transmission / perikaryon / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.49 Å | |||||||||
Authors | Yelshanskaya, M.V. / Li, M. / Sobolevsky, A.I. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2014 Title: Structure of an agonist-bound ionotropic glutamate receptor. Authors: Yelshanskaya, M.V. / Li, M. / Sobolevsky, A.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u4g.cif.gz | 532.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u4g.ent.gz | 439 KB | Display | PDB format |
PDBx/mmJSON format | 4u4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/4u4g ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u4g | HTTPS FTP |
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-Related structure data
Related structure data | 4u4fC 3h5vS 3kg2S 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
#1: Protein | Mass: 92238.320 Da / Num. of mol.: 4 / Fragment: UNP residues 25-847 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491 #2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-ZK1 / {[ |
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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: 4.17 Å3/Da / Density % sol: 70.51 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / Details: 7-11% PEG 20,000, 0.1 M MES / PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4.49→50 Å / Num. obs: 36039 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 206.6 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 4.49→4.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.48 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H5V, 3KG2 Resolution: 4.49→50 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.49→50 Å
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Refine LS restraints |
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LS refinement shell |
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