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- PDB-1syh: X-RAY STRUCTURE OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPL... -
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Basic information
Entry | Database: PDB / ID: 1syh | ||||||
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Title | X-RAY STRUCTURE OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPLEX WITH (S)-CPW399 AT 1.85 A RESOLUTION. | ||||||
![]() | Glutamate receptor 2 | ||||||
![]() | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / LIGAND-BINDING CORE / AGONIST COMPLEX | ||||||
Function / homology | ![]() spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / 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 receptor binding / positive regulation of synaptic transmission / 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 / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / 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 / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Tyr702 Is an Important Determinant of Agonist Binding and Domain Closure of the Ligand-Binding Core of GluR2. Authors: Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Fattorusso, C. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. #1: ![]() 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: ![]() 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: ![]() 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, R. / JIN, R. / GOUAUX, E. | ||||||
History |
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Remark 999 | SEQUENCE TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER ...SEQUENCE TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 115 AND 116) |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.6 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1syiC ![]() 1xhyC ![]() 1m5cS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 1 / Fragment: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CPW / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG8000, cacodylate, (NH4)2SO4 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8111 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 26350 / Num. obs: 26350 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2611 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1M5C Resolution: 1.8→24.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1431157 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 1-2 AND 262-263 WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
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Solvent computation | Solvent model: flat model / Bsol: 45.6 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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