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Yorodumi- PDB-1n0t: X-ray structure of the GluR2 ligand-binding core (S1S2J) in compl... -
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-Basic information
Entry | Database: PDB / ID: 1n0t | ||||||
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Title | X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with the antagonist (S)-ATPO at 2.1 A resolution. | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / antagonist 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 / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / extracellularly glutamate-gated ion channel activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / 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 / 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: 2.1 Å | ||||||
Authors | Hogner, A. / Greenwood, J.R. / Liljefors, T. / Lunn, M.-L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. / Kastrup, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Competitive antagonism of AMPA receptors by ligands of different classes: crystal structure of ATPO bound to the GluR2 ligand-binding core, in comparison with DNQX. Authors: Hogner, A. / Greenwood, J.R. / Liljefors, T. / Lunn, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. / Kastrup, J.S. #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 |
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Remark 999 | Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand-binding ...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 118-119). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). The two first residues (Gly, Ala) are cloning artifacts and were not located in the electron density map. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n0t.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n0t.ent.gz | 189.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n0t_validation.pdf.gz | 632.9 KB | Display | wwPDB validaton report |
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Full document | 1n0t_full_validation.pdf.gz | 646 KB | Display | |
Data in XML | 1n0t_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 1n0t_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/1n0t ftp://data.pdbj.org/pub/pdb/validation_reports/n0/1n0t | HTTPS FTP |
-Related structure data
Related structure data | 1ftlS 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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Details | The biological assembly is a tetramer composed of dimers-of-dimers. In the crystal, only the dimer is observed. The biological dimer can be generated as follows: A, C: 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 1.00000 0.50000 0.00000 -0.50000 B, D: 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 1.00000 0.50000 0.00000 -0.50000 |
-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 4 / Fragment: GluR2-flop ligand-binding core (S1S2J). Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rat / 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-AT1 / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / | #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: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 3350, AMMONIUM SULFATE, SODIUM ACETATE pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 31, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 66583 / Num. obs: 66583 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 59.5 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6551 / % possible all: 98.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 490208 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID CODE 1FTL, molecule A. Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2718199.32 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 1-4 AND 262-263 WERE NOT LOCATED IN THE ELECTRON DENSITY MAP. THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT FULLY DEFINED: LYS A21, MET A25, LYS A69, ARG A149, ARG A163, LYS ...Details: RESIDUES 1-4 AND 262-263 WERE NOT LOCATED IN THE ELECTRON DENSITY MAP. THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT FULLY DEFINED: LYS A21, MET A25, LYS A69, ARG A149, ARG A163, LYS A204, LYS B21, MET B25, LYS B45, ASP B67, LYS B69, ASP B139, ARG B149, LYS B151, ARG B172, LYS C21, GLU C24, LYS C151, LYS D21, GLU D24, LYS D50, ARG D149, LYS D151, ARG D172, LYS D183.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.72 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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