+Open data
-Basic information
Entry | Database: PDB / ID: 5h8n | ||||||
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Title | Structure of the human GluN1/GluN2A LBD in complex with NAM | ||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / GluN1 / GluN2A / NMDA / receptor | ||||||
Function / homology | Function and homology information excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / glutamate receptor signaling pathway / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / Neurexins and neuroligins / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of neuronal synaptic plasticity / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / positive regulation of excitatory postsynaptic potential / ligand-gated monoatomic ion channel activity / Long-term potentiation / monoatomic cation transport / excitatory synapse / calcium ion homeostasis / synaptic cleft / MECP2 regulates neuronal receptors and channels / sensory perception of pain / response to amphetamine / EPHB-mediated forward signaling / excitatory postsynaptic potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / neurogenesis / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / postsynaptic density membrane / brain development / regulation of synaptic plasticity / protein catabolic process / visual learning / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / terminal bouton / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / RAF/MAP kinase cascade / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / dendrite / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wallweber, H.J.A. / Lupardus, P.J. | ||||||
Citation | Journal: Neuron / Year: 2016 Title: Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function. Authors: Hackos, D.H. / Lupardus, P.J. / Grand, T. / Chen, Y. / Wang, T.M. / Reynen, P. / Gustafson, A. / Wallweber, H.J. / Volgraf, M. / Sellers, B.D. / Schwarz, J.B. / Paoletti, P. / Sheng, M. / Zhou, Q. / Hanson, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h8n.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h8n.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/5h8n ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h8n | HTTPS FTP |
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-Related structure data
Related structure data | 5h8fC 5h8hC 5h8qC 5h8sC 5kcjC 2a5tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB
#1: Protein | Mass: 31883.441 Da / Num. of mol.: 1 Fragment: UNP residues 401-539, GT linker, UNP residues 661-802 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12879 |
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#2: Protein | Mass: 33409.074 Da / Num. of mol.: 1 Fragment: UNP residues 394-544, GT linker, UNP residues 663-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05586 |
-Non-polymers , 5 types, 142 molecules
#3: Chemical | ChemComp-GLU / |
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#4: Chemical | ChemComp-5YD / |
#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-GLY / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.72 Å / Num. obs: 21755 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 40.99 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A5T Resolution: 2.5→27.02 Å / Cor.coef. Fo:Fc: 0.9317 / Cor.coef. Fo:Fc free: 0.8965 / SU R Cruickshank DPI: 0.505 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.555 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.269
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Displacement parameters | Biso mean: 30.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→27.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.62 Å / Total num. of bins used: 11
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