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Yorodumi- PDB-3pmv: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -
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-Basic information
Entry | Database: PDB / ID: 3pmv | ||||||
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Title | Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | TRANSPORT PROTEIN / Membrane protein / Fusion protein / chimera protein | ||||||
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 / presynaptic active zone membrane / glutamate-gated receptor activity / 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 / ionotropic glutamate receptor binding / 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 / 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 / perikaryon / postsynaptic membrane / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Maclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. ...Maclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Structure based evolution of a novel series of positive modulators of the AMPA receptor. Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / ...Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pmv.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pmv.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/3pmv ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pmv | HTTPS FTP |
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-Related structure data
Related structure data | 3pmwC 3pmxC 3o28S 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, 1 molecules A
#1: Protein | Mass: 29177.670 Da / Num. of mol.: 1 Fragment: Ligand binding domain, residues 413 to 527 and 653 to 796 Source method: isolated from a genetically manipulated source Details: S1-S2 fusion in which Gly118 and Thr119 replace a membrane-spanning region Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (de3) / References: UniProt: P19491 |
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-Non-polymers , 5 types, 370 molecules
#2: Chemical | ChemComp-GLU / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-557 / | #5: Chemical | ChemComp-GOL / #6: 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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 18% PEG 4000, 50mM Lithium Sulphate, 2.5% Glycerol, 100mM Sodium Cacodylate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2007 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→43.61 Å / Num. all: 24891 / Num. obs: 24891 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2050 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O28 Resolution: 1.8→43.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.149 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.709 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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