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Yorodumi- PDB-1txf: CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE IN COMPLEX WIT... -
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-Basic information
Entry | Database: PDB / ID: 1txf | ||||||
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Title | CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE IN COMPLEX WITH GLUTAMATE AT 2.1 ANGSTROM RESOLUTION | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / 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 ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / 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 / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / glutamatergic synapse / 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: 2.1 Å | ||||||
Authors | Mayer, M.L. | ||||||
Citation | Journal: Neuron / Year: 2005 Title: Crystal structures of the GluR5 and GluR6 ligand binding cores: Molecular mechanisms underlying kainate receptor selectivity Authors: Mayer, M.L. | ||||||
History |
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Remark 999 | SEQUENCE THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE ...SEQUENCE THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUR-5. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER. THE SEQUENCE, AS A RESULT, MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE | ||||||
Remark 300 | BIOMOLECULE THE BIOLOGICAL UNIT IS BELIEVED TO BE A HETEROTETRAMER, THERE IS ONLY ONE MOLECULE IN ...BIOMOLECULE THE BIOLOGICAL UNIT IS BELIEVED TO BE A HETEROTETRAMER, THERE IS ONLY ONE MOLECULE IN THE ASYMMETRIC UNIT AND SYMMETRY OPERATIONS CANNOT BE APPLIED TO GENERATE THE TETRAMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1txf.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1txf.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1txf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1txf_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 1txf_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 1txf_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1txf_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/1txf ftp://data.pdbj.org/pub/pdb/validation_reports/tx/1txf | HTTPS FTP |
-Related structure data
Related structure data | 1s50C 1s7ySC 1s9tC 1sd3C 1tt1C 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
#1: Protein | Mass: 29253.566 Da / Num. of mol.: 1 Fragment: GluR5 ligand binding core (sequence database 446-559 and 682-821) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: pET22 (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B (DE3) / References: UniProt: P22756 |
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#2: Chemical | ChemComp-GLU / |
#3: 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: 3.1 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 10K, 100 mM HEPES, 20 mM NaCl, 1 mM EDTA, 10 mM Glutamate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 21345 / Num. obs: 21345 / % possible obs: 84.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1042 / % possible all: 49.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S7Y Resolution: 2.1→32.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1282416.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.2134 Å2 / ksol: 0.3641 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→32.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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