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- PDB-4f31: Kainate bound to the D655A mutant of the ligand binding domain of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f31 | ||||||
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Title | Kainate bound to the D655A mutant of the ligand binding domain of GluA3 | ||||||
![]() | Glutamate receptor 3 | ||||||
![]() | TRANSPORT PROTEIN/AGONIST / glutamate receptor / GluA3 / GluR3 / AMPA receptor / S1S2 / LBD / neurotransmitter receptor / Kainate / TRANSPORT PROTEIN-AGONIST complex | ||||||
Function / homology | ![]() chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ahmed, A.H. / Oswald, R.E. | ||||||
![]() | ![]() Title: The loss of an electrostatic contact unique to AMPA receptor ligand binding domain 2 slows channel activation. Authors: Holley, S.M. / Ahmed, A.H. / Srinivasan, J. / Murthy, S.E. / Weiland, G.A. / Oswald, R.E. / Nowak, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.7 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 469.2 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f1yC ![]() 4f22C ![]() 4f29C ![]() 4f2oC ![]() 4f2qC ![]() 4f39C ![]() 4f3bC ![]() 4f3gC ![]() 3dlnS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 28926.391 Da / Num. of mol.: 2 / Mutation: D655A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008 |
Radiation | Monochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 16.189 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.28 / Rsym value: 0.496 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DLN Resolution: 2.286→33.731 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 26.1 / 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 / Bsol: 51.401 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.286→33.731 Å
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Refine LS restraints |
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LS refinement shell |
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