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Yorodumi- PDB-4bdm: Crystal structure of the GluK2 K531A LBD dimer in complex with kainate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bdm | ||||||
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Title | Crystal structure of the GluK2 K531A LBD dimer in complex with kainate | ||||||
Components | GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 | ||||||
Keywords | METAL TRANSPORT / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR | ||||||
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 / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / 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 / regulation of membrane potential / 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: 3.4 Å | ||||||
Authors | Nayeem, N. / Mayans, O. / Green, T. | ||||||
Citation | Journal: Open Biol. / Year: 2013 Title: Correlating Efficacy and Desensitization with Gluk2 Ligand-Binding Domain Movements. Authors: Nayeem, N. / Mayans, O. / Green, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bdm.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bdm.ent.gz | 163.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bdm_validation.pdf.gz | 470.8 KB | Display | wwPDB validaton report |
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Full document | 4bdm_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 4bdm_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 4bdm_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/4bdm ftp://data.pdbj.org/pub/pdb/validation_reports/bd/4bdm | HTTPS FTP |
-Related structure data
Related structure data | 4bdlC 4bdnC 4bdoC 4bdqC 4bdrC 1xxrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 29567.842 Da / Num. of mol.: 4 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42260 #2: Chemical | ChemComp-KAI / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 21% PEG 4,000, 9% PROPAN-2-OL, 80MM NA ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→46.97 Å / Num. obs: 14147 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / % possible all: 95.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XXR Resolution: 3.4→46.97 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.81 / SU B: 43.801 / SU ML: 0.656 / Cross valid method: THROUGHOUT / ESU R Free: 0.762 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 34.596 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→46.97 Å
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Refine LS restraints |
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