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Yorodumi- PDB-3ijo: Crystal structure of the AMPA subunit GluR2 bound to the alloster... -
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-Basic information
Entry | Database: PDB / ID: 3ijo | ||||||
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Title | Crystal structure of the AMPA subunit GluR2 bound to the allosteric modulator, althiazide | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / glutamate receptor / glur2 / AMPA receptor / neurotransmitter receptor / S1S2 / allosteric modulator / Alternative splicing / Cell junction / Cell membrane / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / 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 / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.003 Å | ||||||
Authors | Ptak, C.P. / Ahmed, A.H. / Oswald, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Probing the allosteric modulator binding site of GluR2 with thiazide derivatives Authors: Ptak, C.P. / Ahmed, A.H. / Oswald, R.E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ijo.cif.gz | 176.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ijo.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ijo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ijo_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3ijo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3ijo_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 3ijo_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3ijo ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3ijo | HTTPS FTP |
-Related structure data
Related structure data | 3ijxC 3ik6C 3il1C 3iltC 3iluC 3dp6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28808.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2, Gria2; GluR2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #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: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-18 PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 zinc acetate, pH 6.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2008 |
Radiation | Monochromator: RH COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 61344 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Χ2: 2.473 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.36 / Num. unique all: 3012 / Rsym value: 0.698 / Χ2: 1.18 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3dp6 Resolution: 2.003→21.078 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.855 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.54 / σ(I): 0 / 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 / Bsol: 50.594 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.95 Å2 / Biso mean: 32.505 Å2 / Biso min: 0.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.003→21.078 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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