+Open data
-Basic information
Entry | Database: PDB / ID: 3rtw | ||||||
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Title | Nitrowillardiine bound to the ligand binding domain of GluA2 | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | TRANSPORT PROTEIN / glutamate receptor / GluR2 / AMPA receptor / S1S2 / neurotransmitter receptor | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 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 | 3rtw.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rtw.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 3rtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rtw_validation.pdf.gz | 460.7 KB | Display | wwPDB validaton report |
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Full document | 3rtw_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 3rtw_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 3rtw_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/3rtw ftp://data.pdbj.org/pub/pdb/validation_reports/rt/3rtw | HTTPS FTP |
-Related structure data
Related structure data | 3rt6C 3rt8C 3rtfC 3dp6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28835.320 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2, Gria2; GluA2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19491 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 414-527 AND UNP RESIDUES 653-794 CONNECTED BY AN ...PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 414-527 AND UNP RESIDUES 653-794 CONNECTED BY AN ENGINEERED | |
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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: 2.62 Å3/Da / Density % sol: 52.99 % |
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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: Nov 10, 2010 |
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: 2.095→50 Å / Num. all: 47816 / Num. obs: 47765 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 17.157 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2 / Rsym value: 0.654 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DP6 Resolution: 2.095→28.572 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 27.1 / 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: 36.906 Å2 / ksol: 0.347 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.095→28.572 Å
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Refine LS restraints |
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LS refinement shell |
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