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- PDB-4u2r: Crystal structure of the GLUR2 ligand binding core (S1S2J, flip v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u2r | ||||||
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Title | Crystal structure of the GLUR2 ligand binding core (S1S2J, flip variant) in the apo state | ||||||
![]() | Glutamate receptor 2 | ||||||
![]() | Transport protein / Membrane protein / AMPA receptor | ||||||
Function / homology | ![]() 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 / glutamate-gated receptor activity / presynaptic active zone membrane / 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 / 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 / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / 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 / postsynaptic membrane / perikaryon / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Duerr, K.L. / Chen, L. / Gouaux, E. | ||||||
![]() | ![]() Title: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States. Authors: Durr, K.L. / Chen, L. / Stein, R.A. / De Zorzi, R. / Folea, I.M. / Walz, T. / Mchaourab, H.S. / Gouaux, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.8 KB | Display | ![]() |
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PDB format | ![]() | 203.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.9 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 57.3 KB | Display | |
Data in CIF | ![]() | 91.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u1oC ![]() 4u1wC ![]() 4u1xC ![]() 4u1yC ![]() 4u1zC ![]() 4u21C ![]() 4u22C ![]() 4u23C ![]() 4u2pC ![]() 4u2qC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1
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Components
#1: Protein | Mass: 29193.670 Da / Num. of mol.: 4 / Mutation: A796S,A796S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 17-20% PEG8000, 0.2M lithium sulfate, 0.1 M sodium acetate PH range: 4.2-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→63.28 Å / Num. obs: 404918 / % possible obs: 97.3 % / Redundancy: 3.5 % / Net I/σ(I): 8.68 |
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Processing
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Refinement | Resolution: 1.4114→63.28 Å / FOM work R set: 0.7731 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 29.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.56 Å2 / Biso mean: 25.96 Å2 / Biso min: 13.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4114→63.28 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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