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Yorodumi- PDB-4e0w: Crystal structure of the kainate receptor GluK3 ligand binding do... -
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-Basic information
Entry | Database: PDB / ID: 4e0w | ||||||
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Title | Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with kainate | ||||||
Components | Glutamate receptor, ionotropic kainate 3 | ||||||
Keywords | MEMBRANE PROTEIN / ionotropic glutamate receptor / GluK3 / ligand-binding domain / agonist | ||||||
Function / homology | Function and homology information Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / monoatomic ion transmembrane transport / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3501 Å | ||||||
Authors | Venskutonyte, R. / Frydenvang, K. / Kastrup, J.S. | ||||||
Citation | Journal: Neurochem Int / Year: 2012 Title: Kainate induces various domain closures in AMPA and kainate receptors. Authors: Venskutonyte, R. / Frydenvang, K. / Hald, H. / Rabassa, A.C. / Gajhede, M. / Ahring, P.K. / Kastrup, J.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 | 4e0w.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e0w.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 4e0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e0w_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 4e0w_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 4e0w_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4e0w_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/4e0w ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0w | HTTPS FTP |
-Related structure data
Related structure data | 4e0xC 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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Details | A tetrameric multimer representing the known biologically significant oligomerization state of the molecule cannot be generated by symmetry within the crystal. |
-Components
#1: Protein | Mass: 29092.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur7, Grik3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264 | ||||||
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#2: Chemical | ChemComp-KAI / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.8 M SODIUM/POTASSIUM PHOSPHATE, CRYSTALS GROWN IN PRESENCE OF GLUTAMATE SOAKED WITH KAINATE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.478 Å / Num. all: 13287 / Num. obs: 13274 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2 / Rsym value: 0.393 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3S9E Resolution: 2.3501→48.478 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 21.05 / Stereochemistry target values: ML Details: RESIDUES 1-4 (GPGT) WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.155 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3501→48.478 Å
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Refine LS restraints |
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LS refinement shell |
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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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