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- PDB-5tpw: Crystal structure of amino terminal domains of the NMDA receptor ... -
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Open data
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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 | |||||||||
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![]() | TRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION / ZINC INHIBITION | |||||||||
Function / homology | ![]() neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process / conditioned place preference ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process / conditioned place preference / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / sleep / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / regulation of monoatomic cation transmembrane transport / cellular response to lipid / locomotion / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / glutamate binding / cellular response to zinc ion / action potential / spinal cord development / dopamine metabolic process / response to zinc ion / startle response / response to amine / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / modulation of excitatory postsynaptic potential / response to lithium ion / positive regulation of excitatory postsynaptic potential / cellular response to glycine / response to light stimulus / neuron development / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / multicellular organismal response to stress / monoatomic cation channel activity / glutamate-gated receptor activity / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neurogenesis / protein tyrosine kinase binding / response to cocaine / learning / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / response to nicotine / protein catabolic process / calcium channel activity / visual learning / modulation of chemical synaptic transmission / regulation of synaptic plasticity / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / response to organic cyclic compound / terminal bouton / cerebral cortex development / memory / cellular response to growth factor stimulus / response to wounding / response to calcium ion / calcium ion transport / calcium-dependent protein binding / rhythmic process / synaptic vesicle / presynaptic membrane / ATPase binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Romero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.4 KB | Display | ![]() |
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PDB format | ![]() | 177.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.2 KB | Display | ![]() |
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Full document | ![]() | 506.8 KB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tpzC ![]() 5tq0C ![]() 5tq2C ![]() 3qelS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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.) ![]() ![]() ![]() |
-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) ![]() ![]() |
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#4: Antibody | Mass: 23568.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/NAG.gif)
#5: Sugar |
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-Non-polymers , 4 types, 48 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
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#6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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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