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Yorodumi- PDB-4g8n: Crystal structure of the kainate receptor GluK3 ligand-binding do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g8n | ||||||
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Title | Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist G8M | ||||||
Components | Glutamate receptor, ionotropic kainate 3 | ||||||
Keywords | MEMBRANE PROTEIN/Agonist / membrane protein / ionotropic glutamate receptor / ligand binding domain / agonist complex / MEMBRANE PROTEIN-Agonist complex | ||||||
Function / homology | Function and homology information Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Venskutonyte, R. / Kastrup, J.S. / Frydenvang, K. / Gajhede, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Pharmacological and structural characterization of conformationally restricted (S)-glutamate analogues at ionotropic glutamate receptors. Authors: Juknaite, L. / Venskutonyte, R. / Assaf, Z. / Faure, S. / Gefflaut, T. / Aitken, D.J. / Nielsen, B. / Gajhede, M. / Kastrup, J.S. / Bunch, L. / Frydenvang, K. / Pickering, D.S. #1: Journal: J. Struct. Biol. / Year: 2011 Title: Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate. Authors: Venskutonyte, R. / Frydenvang, K. / Gajhede, M. / Bunch, L. / Pickering, D.S. / Kastrup, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g8n.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g8n.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 4g8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g8n_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 4g8n_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 4g8n_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4g8n_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/4g8n ftp://data.pdbj.org/pub/pdb/validation_reports/g8/4g8n | HTTPS FTP |
-Related structure data
Related structure data | 4g8mC 3s9eS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29092.453 Da / Num. of mol.: 1 / Fragment: UNP residues 432-546, 669-806 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 / References: UniProt: P42264 | ||||
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#2: Chemical | ChemComp-G8M / ( | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.2M sodium/potassium phosphate. Crystals were grown in the presence of glutamate and soaked with new ligand G8M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→67.821 Å / Num. all: 13403 / Num. obs: 13403 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 9.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3S9E Resolution: 2.3→29.689 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8552 / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.046 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.07 Å2 / Biso mean: 28.617 Å2 / Biso min: 10.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.689 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %
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