+Open data
-Basic information
Entry | Database: PDB / ID: 3rt6 | ||||||
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Title | Fluorowillardiine bound to the ligand binding domain of GluA3 | ||||||
Components | Glutamate receptor 3 | ||||||
Keywords | TRANSPORT PROTEIN / glutamate receptor / GluR3 / AMPA receptor / S1S2 / neurotransmitter receptor | ||||||
Function / homology | Function and homology information chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / protein homotetramerization / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.836 Å | ||||||
Authors | Ahmed, A.H. / Oswald, R.E. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2011 Title: Mechanisms of Modal Activation of GluA3 Receptors. Authors: Poon, K. / Ahmed, A.H. / Nowak, L.M. / Oswald, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rt6.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rt6.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/3rt6 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/3rt6 | HTTPS FTP |
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-Related structure data
Related structure data | 3rt8C 3rtfC 3rtwC 3dlnS C: citing same article (ref.) S: Starting model for refinement |
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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: 28956.418 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluA3, Glur3, Gria3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19492 |
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#2: Chemical | ChemComp-FWD / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | PROTEIN IS NATURAL ISOFORM FLIP (P19492-2). PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 417-530 AND ...PROTEIN IS NATURAL ISOFORM FLIP (P19492-2). PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 417-530 AND UNP RESIDUES 658-799 CONNECTED BY AN ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14-15% PEG8000, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008 |
Radiation | Monochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.835→50 Å / Num. all: 7886 / Num. obs: 7864 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.179 / Rsym value: 0.179 / Net I/σ(I): 13.323 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 4.024 / Rsym value: 0.568 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DLN Resolution: 2.836→34.304 Å / SU ML: 0.37 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 25.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.341 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.836→34.304 Å
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Refine LS restraints |
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LS refinement shell |
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