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Yorodumi- PDB-4iy5: Crystal structure of the glua2 ligand-binding domain (S1S2J-L483Y... -
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-Basic information
Entry | Database: PDB / ID: 4iy5 | ||||||
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Title | Crystal structure of the glua2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and CX516 at 2.0 A resolution | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | MEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GLUA2 S1S2J-L483Y-N754S / CX516 / ALLOSTERIC MODULATION | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / 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 / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Krintel, C. / Frydenvang, K. / Harpsoe, K. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain Authors: Krintel, C. / Harpsoe, K. / Zachariassen, L.G. / Peters, D. / Frydenvang, K. / Pickering, D.S. / Gajhede, M. / Kastrup, J.S. #1: Journal: Biochem.J. / Year: 2012 Title: Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2. Authors: Krintel, C. / Frydenvang, K. / Olsen, L. / Kristensen, M.T. / de Barrios, O. / Naur, P. / Francotte, P. / Pirotte, B. / Gajhede, M. / Kastrup, J.S. #2: Journal: J.Neurosci. / Year: 2005 Title: Mechanism of positive allosteric modulators acting on AMPA receptors. Authors: Jin, R. / Clark, S. / Weeks, A.M. / Dudman, J.T. / Gouaux, E. / Partin, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iy5.cif.gz | 243.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iy5.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 4iy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iy5 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iy5 | HTTPS FTP |
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-Related structure data
Related structure data | 4iy6C 3tdjS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29244.678 Da / Num. of mol.: 2 Fragment: Ligand binding domain, UNP RESIDUES 413-527, 653-796 Mutation: L94Y, N242S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: P19491 |
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-Non-polymers , 6 types, 586 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CX5 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FUSION PROTEIN OF THE RESIDUES 413-527, LINKER GLY-THR, AND RESIDUES 653-796 FROM GLUA2 |
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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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 24.4% PEG 4000, 0.3M lithium sulfate, 0.1M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 99 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03796 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→26.432 Å / Num. obs: 39394 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TDJ Resolution: 2→26.432 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→26.432 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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Refinement TLS params. | Method: refined / Origin x: 29.3718 Å / Origin y: 16.8211 Å / Origin z: 3.3744 Å
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Refinement TLS group | Selection details: ALL |