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Yorodumi- PDB-6e7u: Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e7u | |||||||||
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Title | Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 | |||||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||
Keywords | TRANSPORT PROTEIN / NMDA Receptor / Ion channel / Allosteric modulation / Extracellular domain | |||||||||
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 / apical dendrite / dendritic branch / positive regulation of inhibitory postsynaptic potential / response to other organism / regulation of ARF protein signal transduction / response to methylmercury / fear response / positive regulation of cysteine-type endopeptidase activity / cellular response to dsRNA / response to carbohydrate / negative regulation of dendritic spine maintenance / interleukin-1 receptor binding / cellular response to lipid / regulation of monoatomic cation transmembrane transport / positive regulation of glutamate secretion / response to growth hormone / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / NMDA selective glutamate receptor complex / 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 / receptor clustering / suckling behavior / behavioral response to pain / startle response / response to amine / small molecule binding / action potential / : / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / associative learning / regulation of MAPK cascade / positive regulation of excitatory postsynaptic potential / response to magnesium ion / cellular response to organic cyclic compound / extracellularly glutamate-gated ion channel activity / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / behavioral fear response / neuron development / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / multicellular organismal response to stress / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / D2 dopamine receptor binding / monoatomic cation channel activity / response to electrical stimulus / synaptic cleft / response to mechanical stimulus / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / cell adhesion molecule binding / cellular response to forskolin / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / response to amphetamine / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / regulation of membrane potential / excitatory postsynaptic potential / response to cytokine / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cocaine / synaptic membrane / synaptic transmission, glutamatergic / hippocampus development / long-term synaptic potentiation / cellular response to amino acid stimulus / 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: 2.27 Å | |||||||||
Authors | Regan, M.C. / Furukawa, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e7u.cif.gz | 577.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e7u.ent.gz | 474.6 KB | Display | PDB format |
PDBx/mmJSON format | 6e7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e7u_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6e7u_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6e7u_validation.xml.gz | 57.7 KB | Display | |
Data in CIF | 6e7u_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/6e7u ftp://data.pdbj.org/pub/pdb/validation_reports/e7/6e7u | HTTPS FTP |
-Related structure data
Related structure data | 6e7rC 6e7sC 6e7tC 6e7vC 6e7wC 6e7xC 3qelS 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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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.) Xenopus laevis (African clawed frog) / Gene: grin1 / Production host: 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.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00960 |
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-Sugars , 2 types, 7 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 , 4 types, 349 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | #8: 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: 3.21 Å3/Da / Density % sol: 61.72 % / 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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.262→35 Å / Num. obs: 92724 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Rrim(I) all: 0.081 / Χ2: 0.846 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QEL Resolution: 2.27→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 14.645 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.229 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: 97.46 Å2 / Biso mean: 39.604 Å2 / Biso min: 10.17 Å2
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Refinement step | Cycle: final / Resolution: 2.27→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: 2.267→2.326 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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