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Yorodumi- PDB-5jty: Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains wi... -
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-Basic information
Entry | Database: PDB / ID: 5jty | ||||||
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Title | Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007 | ||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | ||||||
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 / serotonin metabolic process / EPHB-mediated forward signaling / 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 / serotonin metabolic process / EPHB-mediated forward signaling / 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 / dendritic spine organization / regulation of monoatomic cation transmembrane transport / 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 neuronal synaptic plasticity / regulation of dendrite morphogenesis / dopamine metabolic process / regulation of axonogenesis / spinal cord development / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / ligand-gated monoatomic ion channel activity / associative learning / monoatomic cation transport / excitatory synapse / response to light stimulus / positive regulation of dendritic spine maintenance / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / glutamate receptor binding / regulation of postsynaptic membrane potential / phosphatase binding / calcium ion homeostasis / synaptic cleft / cellular response to manganese ion / prepulse inhibition / regulation of neuron apoptotic process / glutamate-gated receptor activity / 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 / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / 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 / learning / synaptic transmission, glutamatergic / 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: 2.72 Å | ||||||
Authors | Mou, T.-C. / Sprang, S.R. / Hansen, K.B. | ||||||
Citation | Journal: Neuron / Year: 2016 Title: Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors. Authors: Yi, F. / Mou, T.C. / Dorsett, K.N. / Volkmann, R.A. / Menniti, F.S. / Sprang, S.R. / 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 | 5jty.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jty.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/5jty ftp://data.pdbj.org/pub/pdb/validation_reports/jt/5jty | HTTPS FTP |
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-Related structure data
Related structure data | 5i56C 5i57SC 5i58C 5i59C 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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1 |
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Unit cell |
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-Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33340.031 Da / Num. of mol.: 1 / Fragment: unp residues 415-565; 684-821 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: 31533.053 Da / Num. of mol.: 1 / Fragment: unp residues 402-539; 661-800 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 |
-Non-polymers , 4 types, 84 molecules
#3: Chemical | ChemComp-2JK / |
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#4: Chemical | ChemComp-6ND / |
#5: Chemical | ChemComp-GLU / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | The sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in ...The sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in this sequence is a Ser758 in Swiss-Prot Q00959. |
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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: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→14.973 Å / Num. obs: 15868 / % possible obs: 89.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.2 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I57 Resolution: 2.72→14.973 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→14.973 Å
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Refine LS restraints |
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LS refinement shell |
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