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- PDB-3qxm: Crystal Structure of Human GluK2 Ligand-Binding Core in Complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qxm | ||||||
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Title | Crystal Structure of Human GluK2 Ligand-Binding Core in Complex with Novel Marine-Derived Toxins, Neodysiherbaine A | ||||||
![]() | Glutamate receptor ionotropic, kainate 2 | ||||||
![]() | MEMBRANE PROTEIN / two domains / ligand-binding | ||||||
Function / homology | ![]() Activation of Na-permeable kainate receptors / mossy fiber rosette / detection of cold stimulus involved in thermoception / kainate selective glutamate receptor complex / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor signaling pathway / ubiquitin conjugating enzyme binding / Activation of Ca-permeable Kainate Receptor ...Activation of Na-permeable kainate receptors / mossy fiber rosette / detection of cold stimulus involved in thermoception / kainate selective glutamate receptor complex / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor signaling pathway / ubiquitin conjugating enzyme binding / Activation of Ca-permeable Kainate Receptor / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / 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 / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / 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 / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Unno, M. / Sasaki, M. / Ikeda-Saito, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.6 KB | Display | ![]() |
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PDB format | ![]() | 178.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2znsC ![]() 2zntC ![]() 2znuC ![]() 3fuzC ![]() 3fv1C ![]() 3fv2C ![]() 3fvgC ![]() 3fvkC ![]() 3fvnC ![]() 3g3fS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29286.527 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 429-544,UNP RESIDUES 667-806 Source method: isolated from a genetically manipulated source Details: The fusion protein of RESIDUES 429-544 of GluR-6, the linker GLY-THR and 667-806 of GluR-6 Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18-22% PEG4000, 2mM Tris, 1mM EDTA, 10mM NaCl, 10mM Sodium L-ascorbate monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2009 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 67908 / Num. obs: 62566 / % possible obs: 96.11 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible all: 75.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3G3F Resolution: 1.65→29.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.619 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.369 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→29.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 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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