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Yorodumi- PDB-5vij: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vij | |||||||||
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Title | Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist | |||||||||
Function / homology | Function and homology information response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion ...response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / response to morphine / glutamate-gated calcium ion channel activity / cellular response to dsRNA / response to carbohydrate / regulation of monoatomic cation transmembrane transport / dendritic spine organization / cellular response to lipid / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / dopamine metabolic process / spinal cord development / suckling behavior / startle response / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / response to light stimulus / excitatory synapse / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of dendritic spine maintenance / glutamate receptor binding / regulation of postsynaptic membrane potential / phosphatase binding / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / long-term memory / regulation of neuron apoptotic process / glutamate-gated receptor activity / synaptic cleft / presynaptic active zone membrane / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / cell adhesion molecule binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / learning / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å | |||||||||
Authors | Mou, T.-C. / Conti, P. / Pinto, A. / Tamborini, L. / Sprang, S.R. / Hansen, K.B. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits. Authors: Lind, G.E. / Mou, T.C. / Tamborini, L. / Pomper, M.G. / De Micheli, C. / Conti, P. / Pinto, A. / Hansen, K.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vij.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vij.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 5vij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5vij ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vij | HTTPS FTP |
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-Related structure data
Related structure data | 5dexC 5vihC 5viiC 4nf8S 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: 33340.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439 |
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#2: Protein | Mass: 31785.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959 |
#3: Chemical | ChemComp-GLY / |
#4: Chemical | ChemComp-5DX / |
#5: Water | ChemComp-HOH / |
Sequence details | THIS SAMPLE SEQUENCE MATCHES WITH NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonia Acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.105→19.98 Å / Num. obs: 34022 / % possible obs: 98.1 % / Redundancy: 3 % / Rsym value: 0.119 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 2.11→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 2941 / Rsym value: 0.649 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NF8 Resolution: 2.105→19.98 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32 / 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: 2.105→19.98 Å
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Refine LS restraints |
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LS refinement shell |
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