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Yorodumi- PDB-1mqj: Crystal structure of the GluR2 ligand binding core (S1S2J) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqj | ||||||
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Title | Crystal structure of the GluR2 ligand binding core (S1S2J) in complex with willardiine at 1.65 angstroms resolution | ||||||
Components | glutamate receptor 2GRIA2 | ||||||
Keywords | MEMBRANE PROTEIN / ionotropic glutamate receptor / GluR2 / ligand binding core / S1S2 / partial agonist / willardiine | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Jin, R. / Banke, T.G. / Mayer, M.L. / Traynelis, S.F. / Gouaux, E. | ||||||
Citation | Journal: Nat.Neurosci. / Year: 2003 Title: Structural basis for partial agonist action at ionotropic glutamate receptors Authors: Jin, R. / Banke, T.G. / Mayer, M.L. / Traynelis, S.F. / Gouaux, E. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqj.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqj.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqj ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqj | HTTPS FTP |
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-Related structure data
Related structure data | 1mqgC 1mqhC 1mqiSC 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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1 |
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Unit cell |
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Details | The entry contains one molecule which forms a dimer with crystallographic symmetry equivalent molecule in an adjacent asymmetric unit. The symmetry operation is (-x, -y, z) |
-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 / Fragment: ligand binding core (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR-2 or GluR-B / Plasmid: PETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) Keywords: The native GluR2 is a membrane protein. Transmembrane regions were genetically removed and replaced withy a Gly-Thr linker References: UniProt: P19491, UniProt: p19491 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HWD / |
#4: 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: 2.48 Å3/Da / Density % sol: 50.45 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 5K MME, Na Citrate, zinc acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 35502 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.93 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.279 / Num. unique all: 5646 / % possible all: 93.7 |
Reflection shell | *PLUS % possible obs: 93.7 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1mqi Resolution: 1.65→29.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1260625.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.721 Å2 / ksol: 0.387141 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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