[English] 日本語
Yorodumi- PDB-1pb8: CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pb8 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 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 / glutamate-gated receptor activity / synaptic cleft / presynaptic active zone membrane / 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 / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / 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 / memory / synaptic vesicle membrane / cerebral cortex development / intracellular calcium ion homeostasis / neuron cellular homeostasis / response to calcium ion / rhythmic process / calcium ion transport / synaptic vesicle / signaling receptor activity / presynaptic membrane / 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: 1.45 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pb8.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pb8.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 1pb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pb8 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pb8 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-DSN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
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: 1.45→20 Å / Num. all: 52896 / Num. obs: 51309 / % possible obs: 97 % / Observed criterion σ(I): 14.06 / Biso Wilson estimate: 16.3 Å2 |
Reflection shell | Resolution: 1.45→1.5 Å / % possible all: 85.2 |
Reflection | *PLUS Num. measured all: 414093 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 85.2 % / Rmerge(I) obs: 0.172 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→9.99 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2052 Å2 / ksol: 0.465542 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→9.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|