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Yorodumi- PDB-3qem: Crystal structure of amino terminal domains of the NMDA receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qem | |||||||||
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Title | Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981 | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / ion channel / NMDA receptor / allosteric modulation / phenylethanolamine / N-Glycosylation / extracellular / transmembrane | |||||||||
Function / homology | Function and homology information neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / response to hydrogen sulfide ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / response to hydrogen sulfide / Assembly and cell surface presentation of NMDA receptors / regulation of protein kinase A signaling / dendritic branch / response to other organism / positive regulation of inhibitory postsynaptic potential / apical dendrite / regulation of ARF protein signal transduction / fear response / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / cellular response to dsRNA / response to carbohydrate / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / interleukin-1 receptor binding / cellular response to lipid / NMDA glutamate receptor activity / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / NMDA selective glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / glycine binding / response to zinc ion / heterocyclic compound binding / suckling behavior / receptor clustering / startle response / behavioral response to pain / response to amine / small molecule binding / regulation of neuronal synaptic plasticity / action potential / monoatomic cation transmembrane transport / monoatomic cation transport / associative learning / positive regulation of excitatory postsynaptic potential / regulation of MAPK cascade / response to magnesium ion / cellular response to organic cyclic compound / extracellularly glutamate-gated ion channel activity / behavioral fear response / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / D2 dopamine receptor binding / multicellular organismal response to stress / long-term memory / positive regulation of synaptic transmission, glutamatergic / monoatomic cation channel activity / detection of mechanical stimulus involved in sensory perception of pain / synaptic cleft / response to electrical stimulus / response to mechanical stimulus / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / cellular response to forskolin / cell adhesion molecule binding / : / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / cellular response to amino acid stimulus / protein tyrosine kinase binding / regulation of membrane potential / excitatory postsynaptic potential / learning / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cytokine / synaptic membrane / synaptic transmission, glutamatergic / hippocampus development / long-term synaptic potentiation / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / response to nicotine Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å | |||||||||
Authors | Karakas, E. / Simorowski, N. / Furukawa, H. | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors. Authors: Karakas, E. / Simorowski, N. / Furukawa, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qem.cif.gz | 528.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qem.ent.gz | 428.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qem_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3qem_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3qem_validation.xml.gz | 52.9 KB | Display | |
Data in CIF | 3qem_validation.cif.gz | 71.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/3qem ftp://data.pdbj.org/pub/pdb/validation_reports/qe/3qem | HTTPS FTP |
-Related structure data
Related structure data | 3qekSC 3qelC 3jpwS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 42932.055 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain, residues 23-405 / Mutation: N61Q, N371Q 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 #2: Protein | Mass: 41367.902 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain, residues 31-394 / Mutation: N348D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00960 |
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-Sugars , 2 types, 6 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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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: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2010 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 42325 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JPW, 3QEK Resolution: 3.003→29.941 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.96 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.003→29.941 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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