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Yorodumi- PDB-6e7s: Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal dom... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6e7s | |||||||||
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| Title | Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 | |||||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||
Keywords | TRANSPORT PROTEIN / NMDA Receptor / Ion channel / Allosteric modulation / Extracellular domain | |||||||||
| Function / homology | Function and homology informationcellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / sensitization / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / dendritic branch ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / sensitization / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / dendritic branch / response to other organism / regulation of ARF protein signal transduction / fear response / apical dendrite / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to manganese ion / response to carbohydrate / interleukin-1 receptor binding / cellular response to dsRNA / response to growth hormone / cellular response to lipid / negative regulation of dendritic spine maintenance / heterocyclic compound binding / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / positive regulation of glutamate secretion / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / response to zinc ion / protein heterotetramerization / glycine binding / response to amine / regulation of cAMP/PKA signal transduction / small molecule binding / parallel fiber to Purkinje cell synapse / receptor clustering / startle response / monoatomic cation transmembrane transport / behavioral response to pain / regulation of MAPK cascade / response to magnesium ion / regulation of postsynaptic membrane potential / associative learning / action potential / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / response to electrical stimulus / regulation of neuronal synaptic plasticity / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / response to mechanical stimulus / synaptic cleft / neuron development / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / D2 dopamine receptor binding / regulation of long-term synaptic depression / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to cytokine / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cellular response to forskolin / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / protein tyrosine kinase binding / synaptic membrane / response to amphetamine / hippocampal mossy fiber to CA3 synapse / learning / regulation of membrane potential / excitatory postsynaptic potential / response to nicotine / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / hippocampus development / synaptic transmission, glutamatergic / cellular response to amino acid stimulus / regulation of long-term neuronal synaptic plasticity / response to calcium ion / postsynaptic density membrane / cerebral cortex development / beta-catenin binding Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | |||||||||
Authors | Regan, M.C. / Furukawa, H. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2019Title: Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors Authors: Regan, M.C. / Furukawa, H. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6e7s.cif.gz | 585.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6e7s.ent.gz | 481.9 KB | Display | PDB format |
| PDBx/mmJSON format | 6e7s.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6e7s_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 6e7s_full_validation.pdf.gz | 1.5 MB | Display | |
| Data in XML | 6e7s_validation.xml.gz | 55.6 KB | Display | |
| Data in CIF | 6e7s_validation.cif.gz | 73.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/6e7s ftp://data.pdbj.org/pub/pdb/validation_reports/e7/6e7s | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6e7rC ![]() 6e7tC ![]() 6e7uC ![]() 6e7vC ![]() 6e7wC ![]() 6e7xC ![]() 3qelS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
NCS oper:
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Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD
| #1: Protein | Mass: 43162.270 Da / Num. of mol.: 2 / Fragment: Extracellular residues 23-407 / Mutation: N61Q, N371Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplusia ni (cabbage looper) / References: UniProt: A0A1L8F5J9#2: Protein | Mass: 41280.820 Da / Num. of mol.: 2 / Fragment: Extracellular residues 32-394 / Mutation: N348D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Trichoplusia ni (cabbage looper) / References: UniProt: Q00960 |
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-Sugars , 3 types, 10 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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 190 molecules 






| #6: Chemical | | #7: Chemical | ChemComp-CL / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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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: 3.26 Å3/Da / Density % sol: 62.31 % / Description: Plates |
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| Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil |
-Data collection
| Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.91979 Å | ||||||||||||||||||||||||||||||
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2017 | ||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.91979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
| Reflection | Resolution: 2.72→29.88 Å / Num. obs: 56030 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 3QEL Resolution: 2.72→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 29.578 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.641 / ESU R Free: 0.302 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 192.82 Å2 / Biso mean: 73.422 Å2 / Biso min: 26.72 Å2
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| Refinement step | Cycle: final / Resolution: 2.72→25 Å
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| Refine LS restraints |
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| Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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| LS refinement shell | Resolution: 2.72→2.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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About Yorodumi




X-RAY DIFFRACTION
United States, 2items
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PDBj






Trichoplusia ni (cabbage looper)