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Yorodumi- PDB-1mqi: Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Com... -
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-Basic information
Entry | Database: PDB / ID: 1mqi | ||||||
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Title | Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with Fluoro-Willardiine at 1.35 Angstroms Resolution | ||||||
Components | glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / ionotropic glutamate receptor / GluR2 / ligand binding core / S1S2 / partial agonist / willardiines / fluoro-willardiine | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor 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 / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor 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 / glutamate-gated calcium ion channel activity / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor 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 signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / establishment of protein localization / modulation of chemical synaptic transmission / receptor internalization / terminal bouton / 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 / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / endoplasmic reticulum membrane / 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: 1.35 Å | ||||||
Authors | Jin, R. / Banke, T.G. / Mayer, M.L. / Traynelis, S.F. / Gouaux, E. | ||||||
Citation | Journal: Nat.Neurosci. / Year: 2003 Title: Structural basis for partial agonist action at ionotropic glutamate receptors Authors: Jin, R. / Banke, T.G. / Mayer, M.L. / Traynelis, S.F. / Gouaux, E. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqi.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqi.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mqi_validation.pdf.gz | 378.8 KB | Display | wwPDB validaton report |
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Full document | 1mqi_full_validation.pdf.gz | 380.5 KB | Display | |
Data in XML | 1mqi_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1mqi_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqi ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqi | HTTPS FTP |
-Related structure data
Related structure data | 1mqgC 1mqhC 1mqjC 1ftmS 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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Unit cell |
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Details | The entry contains one molecule which forms a dimer with crystallographic symmetry equivalent molecule in an adjacent asymmetric unit. The symmetry operation is (-x, -y, z) |
-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 / Fragment: ligand binding core (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR-2 or GluR-B / Plasmid: PETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) Keywords: The native GluR2 is a membrane protein. Transmembrane regions were genetically removed and replaced withy a Gly-Thr linker References: UniProt: P19491, UniProt: p19491 |
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#2: Chemical | ChemComp-FWD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.03 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8K, NaCl, Na Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9746 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9746 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 57754 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 4.63 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.19 / Num. unique all: 3612 / % possible all: 52.1 |
Reflection | *PLUS % possible obs: 91.1 % |
Reflection shell | *PLUS % possible obs: 52.1 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FTM Resolution: 1.35→29.46 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1277179.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.393 Å2 / ksol: 0.383952 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→29.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rwork: 0.199 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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