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Yorodumi- PDB-3h6w: Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S)... -
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-Basic information
Entry | Database: PDB / ID: 3h6w | ||||||
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Title | Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | MEMBRANE PROTEIN / AMPA receptor ligand-binding core / iGluR2 S1S2J-N754S / 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 / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / 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 / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic 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 / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Hald, H. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Distinct structural features of cyclothiazide are responsible for effects on peak current amplitude and desensitization kinetics at iGluR2. Authors: Hald, H. / Ahring, P.K. / Timmermann, D.B. / Liljefors, T. / Gajhede, M. / Kastrup, J.S. #1: 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. #2: Journal: Nature / Year: 2002 Title: Mechanism of glutamate receptor desensitization. Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h6w.cif.gz | 245.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6w.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 3h6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6w ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6w | HTTPS FTP |
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-Related structure data
Related structure data | 3h6tC 3h6uC 3h6vC 1ftjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29194.658 Da / Num. of mol.: 2 Fragment: iGluR2-flop ligand-binding core: UNP residues 413-796 Mutation: N754S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491 |
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-Non-polymers , 6 types, 691 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | NATIVE IGLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING ...NATIVE IGLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZ |
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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: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→17.38 Å / Num. obs: 72325 / % possible obs: 85.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.49→1.55 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8047 / Rsym value: 0.405 / % possible all: 95.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FTJ Resolution: 1.49→17.38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.661 / SU ML: 0.063 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.098 / 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 max: 57.28 Å2 / Biso mean: 19.9 Å2 / Biso min: 7.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→17.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.53 Å / Total num. of bins used: 20
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