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Yorodumi- PDB-1mqd: X-ray structure of the GluR2 ligand-binding core (S1S2J) in compl... -
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-Basic information
Entry | Database: PDB / ID: 1mqd | ||||||
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Title | X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA at 1.46 A resolution. Crystallization in the presence of lithium sulfate. | ||||||
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 / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / 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 / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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. / Jin, R. / Liljefors, T. / Mayer, M. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqd.cif.gz | 279.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqd.ent.gz | 220 KB | Display | PDB format |
PDBx/mmJSON format | 1mqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqd ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqd | HTTPS FTP |
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-Related structure data
Related structure data | 1ms7C 1m5bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer. The dimer of chain A can be generated by -x, y, -z, shift 1 0 0. The dimer of chain B can be generated by -x, y, -z, shift 0 0 0. The dimer of chain C can be generated by -x, y, -z, shift -1 0 -1. The dimer of chain D can be generated by -x, y, -z, shift 0 0 -1. |
-Components
#1: Protein | Mass: 29077.553 Da / Num. of mol.: 4 / Fragment: GluR2-flop ligand-binding core (S1S2J) Source method: isolated from a genetically manipulated source Details: Tetherd dimer linked by GLY 115 and THR 116 / 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 | #3: Chemical | ChemComp-SHI / ( #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 20% PEG 8000, 0.1M lithium sulfate, 0.1M cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8499 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→20 Å / Num. all: 191888 / Num. obs: 191888 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.46→1.49 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.4 / Num. unique all: 12223 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 95.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M5B Resolution: 1.46→19.24 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1705947 / Data cutoff high rms absF: 1705947 / 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 A1, Lys A18, Lys A66, Lys A104, Lys A126, Glu A129, Glu A142, Arg A146, Lys A180, Lys A246, Lys B1, Lys B18, Glu B21, Glu B24, Ala B63, Asp B64, Lys B66, Glu B119, Lys B126, Glu B142, Lys B255, Lys C1, Lys C47, Arg C61, Asp C64, Lys C66, Lys C126, Glu C129, Glu C142, Arg C146, Lys C148, Arg C180, Lys C246, Lys C255, Lys D1, Lys D18, Met D22, Lys D47, Lys D49, Ala D63, Lys D66, Lys D126, Glu D142
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.86 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.46→19.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 2 % / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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