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Yorodumi- PDB-1my1: crystal titration experiments (AMPA co-crystals soaked in 10 nM BrW) -
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-Basic information
Entry | Database: PDB / ID: 1my1 | ||||||
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Title | crystal titration experiments (AMPA co-crystals soaked in 10 nM BrW) | ||||||
Components | GLUTAMATE RECEPTOR 2 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUR2 / LIGAND BINDING CORE / S1S2 / PARTIAL AGONIST / Bromo-WILLARDIINE / AMPA / crystal titration | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Jin, R. / Gouaux, E. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Probing the Function, Conformational Plasticity, and Dimer-Dimer Contacts of the GluR2 Ligand-Binding Core: Studies of 5-Substituted Willardiines and GluR2 S1S2 in the Crystal Authors: Jin, R. / Gouaux, E. #1: Journal: To be Published Title: PARTIAL AGONIST ACTION DEFINED BY STABILIZATION OF SPECIFIC CONFORMATIONAL SUBSTATES Authors: Jin, R. / Bank, T. / Mayer, M.L. / Traynelis, S. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1my1.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1my1.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 1my1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1my1_validation.pdf.gz | 376.5 KB | Display | wwPDB validaton report |
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Full document | 1my1_full_validation.pdf.gz | 387.9 KB | Display | |
Data in XML | 1my1_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1my1_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/1my1 ftp://data.pdbj.org/pub/pdb/validation_reports/my/1my1 | HTTPS FTP |
-Related structure data
Related structure data | 1mxuC 1mxvC 1mxwC 1mxxC 1mxyC 1mxzC 1my0C 1my2C 1my3C 1my4C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 3 / Fragment: LIGAND BINDING CORE (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PETGQ / 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: 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: 2.54 Å3/Da / Density % sol: 51.61 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, zinc acetate, sodium cacodylate, pH 6.5 and AMPA, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / 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: NSLS / Beamline: X4A / Wavelength: 0.91843 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91843 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 67802 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.133 / % possible all: 74.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Redundancy: 3.5 % |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 74.3 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1FTM Resolution: 1.9→29.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2318541.93 / Data cutoff high rms absF: 2318541.93 / 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: 45.9266 Å2 / ksol: 0.420085 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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