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Yorodumi- PDB-1pb9: CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH ... -
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-Basic information
Entry | Database: PDB / ID: 1pb9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-CYCLOSERINE AT 1.60 ANGSTROMS RESOLUTION | ||||||
Components | N-methyl-D-aspartate Receptor Subunit 1NMDA receptor | ||||||
Keywords | LIGAND BINDING PROTEIN / Ligand binding receptor / rat / NR1 | ||||||
Function / homology | Function and homology information pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange ...pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / voltage-gated monoatomic cation channel activity / response to morphine / glutamate-gated calcium ion channel activity / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / suckling behavior / startle response / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of dendritic spine maintenance / glutamate receptor binding / phosphatase binding / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / long-term memory / regulation of neuron apoptotic process / synaptic cleft / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / learning / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / visual learning / calcium channel activity / terminal bouton / response to organic cyclic compound / cerebral cortex development / memory / synaptic vesicle membrane / intracellular calcium ion homeostasis / response to calcium ion / neuron cellular homeostasis / rhythmic process / calcium ion transport / synaptic vesicle / presynaptic membrane / signaling receptor activity / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / protein-containing complex assembly / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / transcription by RNA polymerase II / postsynaptic density / learning or memory / calmodulin binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Furukawa, H. / Gouaux, E. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core Authors: Furukawa, H. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pb9.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pb9.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pb9 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pb9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33327.035 Da / Num. of mol.: 1 / Fragment: Ligand Binding Core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NMDAR1 / Organ: forebrain / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439 |
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#2: Chemical | ChemComp-4AX / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 1000, sodium cacodylate, lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 39706 / Num. obs: 38432 / % possible obs: 96.8 % / Observed criterion σ(I): 17.31 / Biso Wilson estimate: 19.3 Å2 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 78.3 |
Reflection | *PLUS Num. measured all: 293632 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 78.3 % / Rmerge(I) obs: 0.214 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→10 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.8305 Å2 / ksol: 0.457121 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.1 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.228 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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