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Yorodumi- PDB-1s50: X-ray structure of the GluR6 ligand binding core (S1S2A) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s50 | ||||||
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Title | X-ray structure of the GluR6 ligand binding core (S1S2A) in complex with glutamate at 1.65 A resolution | ||||||
Components | Glutamate Receptor 6 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Mayer, M.L. | ||||||
Citation | Journal: Neuron / Year: 2005 Title: Crystal structures of the GluR5 and GluR6 ligand binding cores: Molecular mechanisms underlying kainate receptor selectivity Authors: Mayer, M.L. | ||||||
History |
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Remark 999 | SEQUENCE THE FIRST GLY IS VECTOR ENCODED. THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN ... SEQUENCE THE FIRST GLY IS VECTOR ENCODED. THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUR-5. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER. THE SEQUENCE, AS A RESULT, MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS BELIEVED TO BE A DIMER, BUT IN THIS CRYSTAL FORM THERE AREN'T ANY SYMMETRY OPERATIONS WHICH GENERATE THE DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s50.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s50.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 1s50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/1s50 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s50 | HTTPS FTP |
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-Related structure data
Related structure data | 1s7ySC 1s9tC 1sd3C 1tt1C 1txfC 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: 29371.633 Da / Num. of mol.: 1 / Fragment: GluR6 ligand binding core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR6 residues 398-513 and 636-775 / Plasmid: pET22 (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P42260 |
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#2: Chemical | ChemComp-GLU / |
#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: 2.31 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% PEG 4000 2 TRIS 20 NaCl 1 EDTA 10 NaGlu , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2003 |
Radiation | Monochromator: monochromator / Protocol: Single Wavelength 0.97946 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 31388 / Num. obs: 31253 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 19.41 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.82 / Num. unique all: 3122 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S7Y (rcsb021380) Resolution: 1.65→27.13 Å / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→27.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.018
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