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Yorodumi- PDB-3bfu: Structure of the ligand-binding core of GluR2 in complex with the... -
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-Basic information
Entry | Database: PDB / ID: 3bfu | ||||||
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Title | Structure of the ligand-binding core of GluR2 in complex with the agonist (R)-TDPA at 1.95 A resolution | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | MEMBRANE PROTEIN / AMPA receptor / GluR2 / ligand-binding core / agonist / (R)-TDPA / Alternative splicing / Cell junction / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / RNA editing / Synapse / Transmembrane / Transport | ||||||
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 / glutamate-gated receptor activity / presynaptic active zone membrane / 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 / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / 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 / perikaryon / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic 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 / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Beich-Frandsen, M. / Mirza, O. / Vestergaard, B. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Structures of the ligand-binding core of iGluR2 in complex with the agonists (R)- and (S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propionic acid explain their unusual equipotency. Authors: Beich-Frandsen, M. / Pickering, D.S. / Mirza, O. / Johansen, T.N. / Greenwood, J. / Vestergaard, B. / Schousboe, A. / Gajhede, M. / Liljefors, T. / Kastrup, J.S. #1: Journal: Neuron / Year: 2000 Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Authors: Armstrong, N. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bfu.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfu.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfu ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfu | HTTPS FTP |
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-Related structure data
Related structure data | 3bftC 1mqdS 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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Unit cell |
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-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 4 / Fragment: residues 1-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PETGQ KANR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P19491 #2: Chemical | ChemComp-R2P / ( #3: 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: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000, cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8122 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8122 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→96.23 Å / Num. obs: 82554 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rsym value: 0.133 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 11970 / Rsym value: 0.506 / % possible all: 99.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MQD Resolution: 1.95→96.23 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.573 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.624 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→96.23 Å
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Refine LS restraints |
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Xplor file |
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