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Yorodumi- PDB-1vso: Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex... -
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-Basic information
Entry | Database: PDB / ID: 1vso | ||||||
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Title | Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex With the Antagonist (S)-ATPO at 1.85 A resolution | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / Antagonist complex | ||||||
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 / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / 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: 1.85 Å | ||||||
Authors | Hald, H. / Naur, P. / Gajhede, M. / Kastrup, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4- ...Title: Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid. Authors: Hald, H. / Naur, P. / Pickering, D.S. / Sprogoe, D. / Madsen, U. / Timmermann, D.B. / Ahring, P.K. / Liljefors, T. / Schousboe, A. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. #1: Journal: FEBS Lett. / Year: 2005 Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate. Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. #2: Journal: J.Neurosci. / Year: 2006 Title: Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists. Authors: Mayer, M.L. / Ghosal, A. / Dolman, N.P. / Jane, D.E. #3: Journal: J.Med.Chem. / Year: 2003 Title: Competitive antagonism of AMPA receptors by ligands of different classes: crystal structure of ATPO bound to the GluR2 ligand-binding core, in comparison with DNQX. Authors: Hogner, A. / Greenwood, J.R. / Liljefors, T. / Lunn, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. / Kastrup, J.S. | ||||||
History |
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Remark 999 | sequence There is a Ala -> Gly sequence conflict at residue 477 in the UniProt database. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). Authors state the functional receptor is a tetramer built of dimers-of-dimers. However, in the crystal only the dimer is present. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vso.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vso.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vso_validation.pdf.gz | 785.7 KB | Display | wwPDB validaton report |
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Full document | 1vso_full_validation.pdf.gz | 787.2 KB | Display | |
Data in XML | 1vso_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1vso_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vso ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vso | HTTPS FTP |
-Related structure data
Related structure data | 2pbwC 1n0tS 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: 29108.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756 |
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#2: Chemical | ChemComp-AT1 / ( |
#3: Chemical | ChemComp-GOL / |
#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 Å3/Da / Density % sol: 59.05 % |
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Crystal grow | Temperature: 279 K / pH: 6.5 Details: 20% PEG 4000, 0.3 M lithium sulfate, 0.1 M cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 13, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. obs: 29461 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.357 / % possible all: 99.9 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N0T, CHAIN A Resolution: 1.85→24.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 229797.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE FULLY REFINED STRUCTURE COMPRISES THR433-GLN492, TRP498-LYS544, THE GLY-THR LINKER, PRO667-SER711 AND SER715-GLY803
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Xplor file |
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