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- PDB-3g3f: Crystal structure of the GluR6 ligand binding domain dimer with g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g3f | ||||||
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Title | Crystal structure of the GluR6 ligand binding domain dimer with glutamate and NaCl at 1.38 Angstrom resolution | ||||||
![]() | Glutamate receptor, ionotropic kainate 2 | ||||||
![]() | MEMBRANE PROTEIN / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Membrane / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport | ||||||
Function / homology | ![]() mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / regulation of membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaudhry, C. / Mayer, M.L. | ||||||
![]() | ![]() Title: Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization. Authors: Chaudhry, C. / Weston, M.C. / Schuck, P. / Rosenmund, C. / Mayer, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.8 KB | Display | ![]() |
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PDB format | ![]() | 185.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g3gC ![]() 3g3hC ![]() 3g3iC ![]() 3g3jC ![]() 3g3kC ![]() 1s7yS 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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Details | The native protein is believed to be a dimer of dimers; only 1 copy of the dimer formed by chains A and B is present in this crystal form. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29371.633 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 Source method: isolated from a genetically manipulated source Details: The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 and 636-775 are coupled by a synthetic GT peptide. The numbering is for the mature protein after cleavage of the 31 AA signal peptide. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 590 molecules ![](data/chem/img/GLU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG4K, 12% isopropanol, 0.1M NaCitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2008 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.377→30 Å / Num. all: 194151 / Num. obs: 194151 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 16.44 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.41 / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S7Y Resolution: 1.377→28.705 Å / SU ML: 0.18 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML Details: Refinement was started with Refmac_5.2. The final rounds of refinement were performed with phenix and included occupancy refinement for ions, and for residues with alternative conformations.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.56 Å2 / ksol: 0.43 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.377→28.705 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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