+Open data
-Basic information
Entry | Database: PDB / ID: 3n6v | ||||||
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Title | Structure of the GluA2 NTD-dimer interface mutant, T78A | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | TRANSPORT PROTEIN / AMPA / assembly / NTD / GluR2 / GluA2 | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / 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 / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Rossmann, M. / Sukumaran, M. / Greger, I.H. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers Authors: Rossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Babu, M.M. / Greger, I.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n6v.cif.gz | 425.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n6v.ent.gz | 347.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/3n6v ftp://data.pdbj.org/pub/pdb/validation_reports/n6/3n6v | HTTPS FTP |
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-Related structure data
Related structure data | 3hsySC 3o2jC 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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Unit cell |
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-Components
#1: Protein | Mass: 42283.797 Da / Num. of mol.: 6 / Fragment: N-terminal domain / Mutation: T78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): TriEx / References: UniProt: P19491 #2: 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: 2.74 Å3/Da / Density % sol: 55.16 % / Mosaicity: 0.58 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100mM Tris, 200mM MgCl2, 20% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→53.776 Å / Num. all: 47323 / Num. obs: 47323 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.158 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 0.9 / Num. measured all: 49741 / Num. unique all: 6789 / Rsym value: 0.635 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HSY Resolution: 3.2→53.776 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.37 / Phase error: 24.82 / 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: 47.216 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 173.6 Å2 / Biso mean: 70.127 Å2 / Biso min: 14.84 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→53.776 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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