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Yorodumi- PDB-2al5: Crystal structure of the GluR2 ligand binding core (S1S2J) in com... -
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-Basic information
Entry | Database: PDB / ID: 2al5 | ||||||
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Title | Crystal structure of the GluR2 ligand binding core (S1S2J) in complex with fluoro-willardiine and aniracetam | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUR2 / LIGAND BINDING CORE / S1S2 / FLUORO-WILLARDIINE / aniracetam / modulator | ||||||
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 / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / 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 / establishment of protein localization / modulation of chemical synaptic transmission / 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 / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / 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: 1.65 Å | ||||||
Authors | Jin, R. / Clark, S. / Weeks, A.M. / Dudman, J.T. / Gouaux, E. / Partin, K.M. | ||||||
Citation | 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. #1: 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. #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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Remark 999 | SEQUENCE The native GluR2 is a membrane protein. Transmembrane regions were genetically removed and ...SEQUENCE The native GluR2 is a membrane protein. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2al5.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2al5.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 2al5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2al5_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 2al5_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 2al5_validation.xml.gz | 28 KB | Display | |
Data in CIF | 2al5_validation.cif.gz | 42.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/2al5 ftp://data.pdbj.org/pub/pdb/validation_reports/al/2al5 | HTTPS FTP |
-Related structure data
Related structure data | 2al4C 1mqiS 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: 29221.682 Da / Num. of mol.: 2 / Fragment: ligand binding core (S1S2J) Mutation: The native GluR2 is a membrane protein. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19491 #2: Chemical | #3: Chemical | ChemComp-4MP / | #4: 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: 2.9 Å3/Da / Density % sol: 57.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12-14% PEG 8000, 0.25-0.35 M ammonium sulfate and 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 86393 / Num. obs: 70497 / % possible obs: 81.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.449 / % possible all: 48.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MQI Resolution: 1.65→26.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1572353.29 / 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: 46.1548 Å2 / ksol: 0.374773 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→26.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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