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Yorodumi- PDB-1wvj: Exploring the GluR2 ligand-binding core in complex with the bicyc... -
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-Basic information
Entry | Database: PDB / ID: 1wvj | ||||||
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Title | Exploring the GluR2 ligand-binding core in complex with the bicyclic AMPA analogue (S)-4-AHCP | ||||||
Components | ionotropic glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / complex with bicyclic AMPA analogue | ||||||
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 / receptor internalization / terminal bouton / 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 / Resolution: 1.75 Å | ||||||
Authors | Nielsen, B.B. / Pickering, D.S. / Greenwood, J.R. / Brehm, L. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. | ||||||
Citation | Journal: FEBS J. / Year: 2005 Title: Exploring the GluR2 ligand-binding core in complex with the bicyclical AMPA analogue (S)-4-AHCP Authors: Nielsen, B.B. / Pickering, D.S. / Greenwood, J.R. / Brehm, L. / Gajhede, M. / Schousboe, A. / 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.K. / 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: 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, Y. / Jin, R. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvj.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvj.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 1wvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wvj_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 1wvj_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 1wvj_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1wvj_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvj ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvj | HTTPS FTP |
-Related structure data
Related structure data | 1m5cS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Flop ligand-binding core of GluR2(GluR2-S1S2J) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IBC / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 3350, phosphate-citrate buffer, lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20.08 Å / Num. all: 27472 / Num. obs: 27472 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.037 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 4.1 / Num. unique all: 1333 / Rsym value: 0.227 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M5C Resolution: 1.75→20.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.37 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The side chains of the following residues are not fully defined: LYS A4, LYS A21, GLU A24, GLU A27, LYS A50, LYS A52, ARG A64, ALA A66, ASP A67, LYS A69, LYS A82, GLU A125, LYS A129, THR ...Details: The side chains of the following residues are not fully defined: LYS A4, LYS A21, GLU A24, GLU A27, LYS A50, LYS A52, ARG A64, ALA A66, ASP A67, LYS A69, LYS A82, GLU A125, LYS A129, THR A131, GLU A145, ARG A148, ARG A149, LYS A151, LYS A157, ARG A172, GLU A176, LYS A183, LYS A204, LYS A240 and GLU A243.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.624 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.754→1.8 Å / Total num. of bins used: 20
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