[English] 日本語
![](img/lk-miru.gif)
- PDB-4f2o: Quisqualate bound to the D655A mutant of the ligand binding domai... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4f2o | ||||||
---|---|---|---|---|---|---|---|
Title | Quisqualate 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 / quisqualate / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 74 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f1yC ![]() 4f22C ![]() 4f29C ![]() 4f2qC ![]() 4f31C ![]() 4f39C ![]() 4f3bC ![]() 4f3gC ![]() 3dlnS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 28926.391 Da / Num. of mol.: 1 / Mutation: D655A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-QUS / ( |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.21 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2009 |
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: 1.9→50 Å / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 19.646 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.93 / Rsym value: 0.436 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3DLN Resolution: 1.912→21.089 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 22.02 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.484 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.912→21.089 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|