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Yorodumi- PDB-4o3c: Crystal structure of the GLUA2 ligand-binding domain in complex w... -
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-Basic information
Entry | Database: PDB / ID: 4o3c | ||||||
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Title | Crystal structure of the GLUA2 ligand-binding domain in complex with L-aspartate at 1.50 A resolution | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | membrane protein/agonist / AMPA RECEPTOR LIGAND-BINDING DOMAIN / GLUA2 / AGONIST / MEMBRANE PROTEIN / membrane protein-agonist complex | ||||||
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 / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / extracellularly glutamate-gated ion channel activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein 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 / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Krintel, C. / Frydenvang, K. / Kaern, A.M. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain. Authors: Krintel, C. / Frydenvang, K. / Ceravalls de Rabassa, A. / Kaern, A.M. / Gajhede, M. / Pickering, D.S. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o3c.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o3c.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 4o3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o3c_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 4o3c_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 4o3c_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4o3c_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o3c ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o3c | HTTPS FTP |
-Related structure data
Related structure data | 4o3aC 4o3bC 1m5cS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 Fragment: Ligand binding domain (unp residues 413-527 and unp residues 653-796) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491 |
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-Non-polymers , 7 types, 278 molecules
#2: Chemical | ChemComp-ASP / | ||
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#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | ChemComp-ACT / | ||
#6: Chemical | ChemComp-LI / | ||
#7: Chemical | ChemComp-SO4 / #8: 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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 4000, 0.1 M lithium sulfate and 0.1 M phosphate-citrate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→28.7 Å / Num. all: 43268 / Num. obs: 43268 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.171 Å2 / Rsym value: 0.055 / Net I/σ(I): 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 43.83 / 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: starting model 1M5C Resolution: 1.5→26.64 Å / Occupancy max: 1 / Occupancy min: 0.25 / Isotropic thermal model: anisotropic (not including water) / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML Details: Refinement done with riding hydrogen atoms and anisotropic B-factors (not including water).
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Displacement parameters | Biso max: 54.05 Å2 / Biso mean: 17.9144 Å2 / Biso min: 6.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→26.64 Å
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Refine LS restraints |
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LS refinement shell |
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