[English] 日本語
Yorodumi- PDB-1ms7: X-ray structure of the GluR2 ligand-binding core (S1S2J) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ms7 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA at 1.97 A resolution, Crystallization in the presence of zinc acetate | ||||||
Components | Glutamate receptor subunit 2 | ||||||
Keywords | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / 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 / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel 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 binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / postsynaptic density membrane / modulation of chemical synaptic transmission / establishment of protein localization / 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 / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / 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 / Resolution: 1.97 Å | ||||||
Authors | Kasper, C. / Lunn, M.-L. / Liljefors, T. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S. | ||||||
Citation | Journal: FEBS Lett. / Year: 2002 Title: GluR2 ligand-binding core complexes: importance of the isoxazolol moiety and 5-substituent for the binding mode of AMPA-type agonists Authors: Kasper, C. / Lunn, M.-L. / Liljefors, T. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-binding Core Authors: Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I. / Gouaux, E. #2: 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. #3: Journal: Nature / Year: 2002 Title: Mechanism of glutamate receptor desensitization Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. #4: Journal: Protein Sci. / Year: 1998 Title: Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct Authors: Chen, G.Q. / Sun, Y. / Jin, R. / Gouaux, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ms7.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ms7.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ms7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ms7_validation.pdf.gz | 400.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ms7_full_validation.pdf.gz | 410.2 KB | Display | |
Data in XML | 1ms7_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1ms7_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1ms7 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1ms7 | HTTPS FTP |
-Related structure data
Related structure data | 1mqdSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The biological assembly is a dimer. Chain A and chain C' (symmetry related: -x, -y, z, shift -1 0 0) form a non-crystallographic dimer. The dimer of chain B can be generated by the two-fold axis: -x, -y, z, shift 0 -1 0. |
-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 3 / Fragment: GluR2-flop ligand-binding core (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 17% PEG 8000, 0.05M zinc acetate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8456 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 17, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8456 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→20 Å / Num. all: 62567 / Num. obs: 62567 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.97→2.02 Å / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3893 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 5.2 % |
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MQD Resolution: 1.97→16.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 2413200 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The first three N-terminal residues and the last two C-terminal residues were not located in the electron density map. The side chains of the following residues are not fully defined: Lys ...Details: The first three N-terminal residues and the last two C-terminal residues were not located in the electron density map. The side chains of the following residues are not fully defined: Lys A18, Glu A24, Glu A27, Lys A47, Glu A122, Gln A127, Glu A142, Lys A148, Lys A154, Glu A163, Lys A237, Lys A246, Lys A255, Glu B24, Ala B63, Asp B64, Lys B66, Glu B142, Lys B148, Lys B246, Lys B255, Lys C18, Glu C21, Glu C24, Lys C42, Asp C64, Lys C66, Arg C169, Lys C255
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.6754 Å2 / ksol: 0.428266 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→16.56 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.212 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|