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Yorodumi- PDB-2znu: Crystal structure of the ligand-binding core of the human ionotro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2znu | ||||||
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Title | Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with a novel selective agonist, neodysiherbaine A | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / GluR5 / ligand-binding core / neodysiherbaine A / agonist / Alternative splicing / Cell junction / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Polymorphism / Postsynaptic cell membrane / RNA editing / Synapse / Transmembrane / Transport | ||||||
Function / homology | Function and homology information Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / central nervous system development / postsynaptic density membrane / modulation of chemical synaptic transmission / nervous system development / presynaptic membrane / chemical synaptic transmission / intracellular membrane-bounded organelle / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Unno, M. / Sasaki, M. / Ikeda-Saito, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors. Authors: Unno, M. / Shinohara, M. / Takayama, K. / Tanaka, H. / Teruya, K. / Doh-Ura, K. / Sakai, R. / Sasaki, M. / Ikeda-Saito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2znu.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2znu.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 2znu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/2znu ftp://data.pdbj.org/pub/pdb/validation_reports/zn/2znu | HTTPS FTP |
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-Related structure data
Related structure data | 2znsSC 2zntC 3fuzC 3fv1C 3fv2C 3fvgC 3fvkC 3fvnC 3qxmC 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: 29093.441 Da / Num. of mol.: 1 Fragment: ligand-binding domain, UNP residues 445-559, UNP residues 682-820 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIK1, GLUR5 / Plasmid: PpCold-I DNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39086 | ||
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#2: Chemical | ChemComp-NDZ / ( | ||
#3: Chemical | ChemComp-BME / #4: 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: 3.18 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG3350, NaCl, EDTA, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 33702 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.056 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.87 / Num. unique all: 3245 / Rsym value: 0.294 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZNS Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.315 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.816 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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