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- 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 | |||||||||
![]() | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||
![]() | TRANSPORT PROTEIN / NMDA Receptor / Ion channel / Allosteric modulation / Extracellular domain | |||||||||
Function / homology | ![]() 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 / Assembly and cell surface presentation of NMDA receptors ...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 / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / 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 / glutamate-gated calcium ion channel activity / 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 / protein heterotetramerization / glutamate binding / action potential / glycine binding / heterocyclic compound binding / response to zinc ion / suckling behavior / startle response / behavioral response to pain / response to amine / monoatomic cation transmembrane transport / receptor clustering / monoatomic cation transport / regulation of neuronal synaptic plasticity / 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 / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / behavioral fear response / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / small molecule binding / cellular response to manganese ion / glutamate receptor binding / D2 dopamine receptor binding / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to mechanical stimulus / 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 signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / response to cocaine / learning / synaptic membrane / response to cytokine / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / hippocampus development / long-term synaptic potentiation / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / response to nicotine Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Regan, M.C. / Furukawa, H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 585.4 KB | Display | ![]() |
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PDB format | ![]() | 481.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 55.6 KB | Display | |
Data in CIF | ![]() | 73.7 KB | Display | |
Arichive directory | ![]() ![]() | 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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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.) ![]() ![]() #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.) ![]() ![]() ![]() |
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-Sugars , 3 types, 10 molecules ![](data/chem/img/NAG.gif)
#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 ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HZ4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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: ![]() Starting 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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