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Yorodumi- PDB-3h5w: Crystal structure of the GluR2-ATD in space group P212121 without... -
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-Basic information
Entry | Database: PDB / ID: 3h5w | ||||||
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Title | Crystal structure of the GluR2-ATD in space group P212121 without solvent | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | TRANSPORT PROTEIN / Glutamate receptor / Ligand-gated ion channel / synapse / Alternative splicing / Cell junction / Cell membrane / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / Receptor / RNA editing / Transmembrane / Transport | ||||||
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: 2.686 Å | ||||||
Authors | Jin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A. / Zhou, J. / Jin, Y. / Gouaux, E. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Crystal structure and association behaviour of the GluR2 amino-terminal domain. Authors: Jin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A.I. / Zhou, J. / Jin, Y. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h5w.cif.gz | 292.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h5w.ent.gz | 236.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h5w_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 3h5w_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 3h5w_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3h5w_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h5w ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h5w | HTTPS FTP |
-Related structure data
Related structure data | 3h5vSC 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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-Components
#1: Protein | Mass: 44509.250 Da / Num. of mol.: 2 / Fragment: UNP residues 21-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491 |
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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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3000, 100mM tri-sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→50 Å / Num. obs: 24737 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.68→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H5V Resolution: 2.686→19.96 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 29.67 / Stereochemistry target values: ML Details: A HIGHER RESOLUTION STRUCTURE OF THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM HAS BEEN DEPOSITED IN PDB AS 3H5V. THE CONFORMATION OF THE PROTOMERS IN 3H5W IS SIMILAR TO THAT OF THE PROTOMERS ...Details: A HIGHER RESOLUTION STRUCTURE OF THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM HAS BEEN DEPOSITED IN PDB AS 3H5V. THE CONFORMATION OF THE PROTOMERS IN 3H5W IS SIMILAR TO THAT OF THE PROTOMERS IN THE HIGHER RESOLUTION, WELL REFINED 3H5V, AND THUS FURTHER REFINEMENT OF THIS CRYSTAL FORM WAS NOT PURSUED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.423 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.686→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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