+Open data
-Basic information
Entry | Database: PDB / ID: 5l1b | ||||||
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Title | AMPA subtype ionotropic glutamate receptor GluA2 in Apo state | ||||||
Components | Glutamate receptor 2,Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / Transporter / fusion protein | ||||||
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: 4 Å | ||||||
Authors | Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Sobolevsky, A.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Neuron / Year: 2016 Title: Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs. Authors: Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Narangoda, C. / Kurnikova, M. / Sobolevsky, A.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l1b.cif.gz | 546.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l1b.ent.gz | 455.8 KB | Display | PDB format |
PDBx/mmJSON format | 5l1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/5l1b ftp://data.pdbj.org/pub/pdb/validation_reports/l1/5l1b | HTTPS FTP |
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-Related structure data
Related structure data | 5l1eC 5l1fC 5l1gC 5l1hC 3kg2S 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: 89805.734 Da / Num. of mol.: 4 Fragment: UNP residues 25-847, with deletions of 397-398, 402-405, 566-587,UNP residues 25-847, with deletions of 397-398, 402-405, 566-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: Embryoni kidney cell / Gene: Gria2, Glur2 / Plasmid: pEG BacMam / Cell line (production host): HEK293 GnTI / Production host: Homo sapiens (human) / References: UniProt: P19491 #2: Sugar | ChemComp-NAG / |
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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: 4.41 Å3/Da / Density % sol: 72.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 8-11% (w/v) PEG 8,000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate (pH 6.3-6.7) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4→48.55 Å / Num. obs: 50426 / % possible obs: 98 % / Observed criterion σ(I): 1.14 / Redundancy: 3.27 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.573 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KG2 Resolution: 4→48.55 Å / SU ML: 0.88 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→48.55 Å
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Refine LS restraints |
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LS refinement shell |
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