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Yorodumi- PDB-1syi: X-RAY STRUCTURE OF THE Y702F MUTANT OF THE GLUR2 LIGAND-BINDING C... -
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-Basic information
Entry | Database: PDB / ID: 1syi | ||||||
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Title | X-RAY STRUCTURE OF THE Y702F MUTANT OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPLEX WITH (S)-CPW399 AT 2.1 A RESOLUTION. | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / LIGAND-BINDING CORE / AGONIST COMPLEX / MUTANT | ||||||
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 / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel 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 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 / modulation of chemical synaptic transmission / establishment of protein localization / 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 / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / 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 | Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2005 Title: Tyr702 Is an Important Determinant of Agonist Binding and Domain Closure of the Ligand-Binding Core of GluR2. Authors: Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Fattorusso, C. / 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. / 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, R. / JIN, R. / GOUAUX, E. | ||||||
History |
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Remark 999 | SEQUENCE TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER ...SEQUENCE TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 115 AND 116) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1syi.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1syi.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 1syi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/1syi ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1syi | HTTPS FTP |
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-Related structure data
Related structure data | 1syhSC 1xhyC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 29205.682 Da / Num. of mol.: 2 / Fragment: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J) / Mutation: Y702F 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 | #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: 2.31 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, CACODYLATE, (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8111 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8111 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 28467 / Num. obs: 28467 / % possible obs: 92.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2794 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1SYH Resolution: 2.1→19.42 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1812154 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 1-2 AND 262-263 WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
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Solvent computation | Solvent model: flat model / Bsol: 53.5 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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