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Yorodumi- PDB-6uz6: Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uz6 | |||||||||
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Title | Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and glutamate | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / NMDAR / ligand-binding domain / agonist | |||||||||
Function / homology | Function and homology information neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / conditioned place preference / response to hydrogen sulfide / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / response to other organism / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / cellular response to magnesium ion / regulation of ARF protein signal transduction / sleep / response to methylmercury / voltage-gated monoatomic cation channel activity / dendritic spine organization / cellular response to dsRNA / response to carbohydrate / regulation of monoatomic cation transmembrane transport / cellular response to lipid / NMDA glutamate receptor activity / locomotion / response to morphine / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / cellular response to zinc ion / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of axonogenesis / regulation of dendrite morphogenesis / male mating behavior / dopamine metabolic process / spinal cord development / suckling behavior / startle response / response to amine / regulation of neuronal synaptic plasticity / action potential / monoatomic cation transmembrane transport / monoatomic cation transport / modulation of excitatory postsynaptic potential / response to lithium ion / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / response to light stimulus / positive regulation of protein targeting to membrane / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / postsynaptic density, intracellular component / cellular response to manganese ion / neurogenesis / glutamate receptor binding / multicellular organismal response to stress / long-term memory / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / monoatomic cation channel activity / calcium ion homeostasis / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / cell adhesion molecule binding / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Wang, J.X. / Furukawa, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors. Authors: Wang, J.X. / Irvine, M.W. / Burnell, E.S. / Sapkota, K. / Thatcher, R.J. / Li, M. / Simorowski, N. / Volianskis, A. / Collingridge, G.L. / Monaghan, D.T. / Jane, D.E. / Furukawa, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uz6.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uz6.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uz6_validation.pdf.gz | 334.6 KB | Display | wwPDB validaton report |
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Full document | 6uz6_full_validation.pdf.gz | 334.6 KB | Display | |
Data in XML | 6uz6_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 6uz6_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/6uz6 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/6uz6 | HTTPS FTP |
-Related structure data
Related structure data | 6uzgC 6uzrC 6uzwC 6uzxC 4nf8S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 33340.031 Da / Num. of mol.: 1 Fragment: ligand-binding domain (UNP residues 415-565,684-821) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439 |
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#2: Protein | Mass: 31606.236 Da / Num. of mol.: 1 Fragment: ligand-binding domain (UNP residues 402-539,661-800) Mutation: A414R, K738M, G740R, R741K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / References: UniProt: Q00959 |
#3: Chemical | ChemComp-GLY / |
#4: Chemical | ChemComp-GLU / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % / Description: long rod-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92013 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92013 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→73.1 Å / Num. obs: 71406 / % possible obs: 96.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 3.9 % / Num. unique obs: 5481 / CC1/2: 0.515 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NF8 Resolution: 1.66→50.07 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.333
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→50.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 40.641021733 Å / Origin y: 75.7939187105 Å / Origin z: 25.8618815501 Å
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Refinement TLS group | Selection details: all |