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Yorodumi- PDB-5tpw: Crystal structure of amino terminal domains of the NMDA receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tpw | |||||||||
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Title | Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION / ZINC INHIBITION | |||||||||
Function / homology | Function and homology information response to ammonium ion / directional locomotion / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / protein localization to postsynaptic membrane / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity ...response to ammonium ion / directional locomotion / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / protein localization to postsynaptic membrane / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / 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 / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / glutamate binding / cellular response to zinc ion / action potential / dopamine metabolic process / spinal cord development / response to zinc ion / startle response / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / glutamate receptor binding / regulation of postsynaptic membrane potential / cellular response to manganese ion / glutamate-gated receptor activity / response to fungicide / monoatomic cation channel activity / sensory perception of pain / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / cell adhesion molecule binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / 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 / protein catabolic process / regulation of synaptic plasticity / modulation of chemical synaptic transmission / visual learning / cytoplasmic vesicle membrane / calcium channel activity / terminal bouton / negative regulation of protein catabolic process / response to organic cyclic compound / memory / cerebral cortex development / cellular response to growth factor stimulus / response to wounding / response to calcium ion / rhythmic process / calcium ion transport / synaptic vesicle / presynaptic membrane / ATPase binding / chemical synaptic transmission / postsynapse / scaffold protein binding / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / signaling receptor binding / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) Rattus norvegicus (Norway rat) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.909 Å | |||||||||
Authors | Romero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Neuron / Year: 2016 Title: Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Authors: Romero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tpw.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tpw.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpw ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpw | HTTPS FTP |
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-Related structure data
Related structure data | 5tpzC 5tq0C 5tq2C 3qelS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43546.734 Da / Num. of mol.: 1 / Fragment: residues 24-408 / Mutation: N38Q, N348Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS |
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#2: Protein | Mass: 40572.078 Da / Num. of mol.: 1 / Fragment: residues 34-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00959 |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 23993.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#4: Antibody | Mass: 23568.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Sugars , 1 types, 2 molecules
#5: Sugar |
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-Non-polymers , 4 types, 48 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: 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: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8M Ammonium sulfate 2.5% Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.2825 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2825 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 55256 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 26.14 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QEL Resolution: 2.909→47.563 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.42 Å2 / Biso mean: 48.9365 Å2 / Biso min: 6.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.909→47.563 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: 30
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