[English] 日本語
Yorodumi- PDB-5tpz: Crystal structure of amino terminal domains of the NMDA receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tpz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in apo closed state | |||||||||
Components |
| |||||||||
Keywords | TRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION | |||||||||
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 / 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 / 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 / glutamate binding / protein heterotetramerization / glycine binding / response to zinc ion / heterocyclic compound binding / suckling behavior / receptor clustering / startle response / behavioral response to pain / response to amine / small molecule binding / regulation of neuronal synaptic plasticity / action potential / monoatomic cation transmembrane transport / monoatomic cation transport / 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 / behavioral fear response / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / D2 dopamine receptor binding / multicellular organismal response to stress / long-term memory / positive regulation of synaptic transmission, glutamatergic / monoatomic cation channel activity / detection of mechanical stimulus involved in sensory perception of pain / synaptic cleft / response to electrical stimulus / response to mechanical stimulus / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / 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 binding / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / cellular response to amino acid stimulus / protein tyrosine kinase binding / regulation of membrane potential / excitatory postsynaptic potential / learning / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cytokine / synaptic membrane / synaptic transmission, glutamatergic / hippocampus development / long-term synaptic potentiation / 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: 3.095 Å | |||||||||
Authors | Romero-Hernandez, A. / Simorwski, N. / Karakas, E. / Furukawa, H. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Neuron / Year: 2016 Title: Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Authors: Romero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tpz.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tpz.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 5tpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tpz_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5tpz_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 5tpz_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 5tpz_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpz ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpz | HTTPS FTP |
-Related structure data
Related structure data | 5tpwC 5tq0C 5tq2C 3qelS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42932.055 Da / Num. of mol.: 1 / Fragment: residues 23-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS | ||
---|---|---|---|
#2: Protein | Mass: 41149.625 Da / Num. of mol.: 1 / Fragment: residues 32-393 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 | ||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG 3350, 1.4M Sodium formate, 0.3M Sodium thyocyanate, 0.1M sodium acetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→37.891 Å / Num. obs: 18198 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QEL Resolution: 3.095→37.891 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.42
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.19 Å2 / Biso mean: 86.3075 Å2 / Biso min: 48.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.095→37.891 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
|