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Yorodumi- PDB-4u2p: Full-length AMPA subtype ionotropic glutamate receptor GluA2 in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u2p | ||||||
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Title | Full-length AMPA subtype ionotropic glutamate receptor GluA2 in the apo state | ||||||
Components | Glutamate receptor 2GRIA2 | ||||||
Keywords | Transport protein / Membrane protein / AMPA receptor | ||||||
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 / Resolution: 3.2386 Å | ||||||
Authors | Duerr, K.L. / Gouaux, E. | ||||||
Citation | Journal: Cell / Year: 2014 Title: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States. Authors: Durr, K.L. / Chen, L. / Stein, R.A. / De Zorzi, R. / Folea, I.M. / Walz, T. / Mchaourab, H.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 | 4u2p.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4u2p.ent.gz | 974.9 KB | Display | PDB format |
PDBx/mmJSON format | 4u2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/4u2p ftp://data.pdbj.org/pub/pdb/validation_reports/u2/4u2p | HTTPS FTP |
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-Related structure data
Related structure data | 4u1oC 4u1wC 4u1xC 4u1yC 4u1zC 4u21C 4u22C 4u23C 4u2qC 4u2rC 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: 92386.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnTI- / References: UniProt: P19491 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-MES / |
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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: 3.84 Å3/Da / Density % sol: 67.95 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES, 5.8-6.2% PEG6000, 5% TMAO, 0.1-0.3 M sodium acetate PH range: pH 6.2-6.5 |
-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 315r / Detector: CCD / Date: Jul 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.002 Å / Num. obs: 65917 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 107.69 Å2 / Net I/σ(I): 7.77 |
-Processing
Software |
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Refinement | Resolution: 3.2386→49.002 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 33.07 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2386→49.002 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.7617 Å / Origin y: 158.9574 Å / Origin z: 90.585 Å
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Refinement TLS group | Selection details: all |