[English] 日本語
Yorodumi- PDB-2aix: X-ray structure of the GLUR2 ligand-binding core (S1S2J) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aix | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the GLUR2 ligand-binding core (S1S2J) in complex with (s)-thio-atpa at 2.2 a resolution. | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / LIGAND-BINDING CORE / AGONIST COMPLEX. | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / 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 / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / 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 / Resolution: 2.17 Å | ||||||
Authors | Kastrup, J.S. | ||||||
Citation | Journal: To be Published Title: Distinct kinetics of ionotropic glutamate receptor 2 splice variants characterized by fast agonist application and crystallization of a receptor-ligand complex. Authors: Holm, M.M. / Lunn, M.L. / Traynelis, S.F. / Kastrup, J.S. / Egebjerg, J. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Structural Basis for Ampa Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the Glur2 Ligand Binding Core. Authors: Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I. / Gouaux, E. #2: 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. #3: Journal: Nature / Year: 2002 Title: Mechanism of Glutamate Receptor Desensitization. Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. #4: Journal: Protein Sci. / Year: 1998 Title: Probing the Ligand Binding Domain of the Glur2 Receptor by Proteolysis and Deletion Mutagenesis Defines Domain Boundaries and Yields a Crystallizable Construct. Authors: Chen, G.Q. / Sun, R. / Jin, R. / Gouaux, E. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE RECEPTOR CONSISTS OF FOUR SUBUNITS CONSTITUTING A TETRAMER. ONE DIMER OF THE TETRAMER CAN BE GENERATED IN THE CRYSTAL. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). | ||||||
Remark 999 | SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand- ...SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand-binding core of GluR2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residues 115-116). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2aix.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2aix.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 2aix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aix_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2aix_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 2aix_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2aix_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2aix ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2aix | HTTPS FTP |
-Related structure data
Related structure data | 1m5bS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 / Fragment: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J). Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491 |
---|---|
#2: Chemical | ChemComp-U1K / ( |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.8 % |
---|---|
Crystal grow | Temperature: 279 K / pH: 6.5 Details: SODIUM CHLORIDE, CACODYLATE, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0835 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0835 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→20 Å / Num. obs: 15624 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.17→2.25 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.6 / % possible all: 93.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M5B. Resolution: 2.17→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1987987.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE FIRST THREE N-TERMINAL RESIDUES AND THE LAST TWO C-TERMINAL RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3512 Å2 / ksol: 0.414103 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.17→2.31 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|