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Yorodumi- PDB-3c34: Crystal structure of GluR5 ligand-binding core in complex with ru... -
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-Basic information
Entry | Database: PDB / ID: 3c34 | ||||||
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Title | Crystal structure of GluR5 ligand-binding core in complex with rubidium at 1.82 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.82 Å | ||||||
Authors | Mayer, M.L. | ||||||
Citation | Journal: Neuron / Year: 2008 Title: Molecular basis of kainate receptor modulation by sodium. Authors: Plested, A.J. / Vijayan, R. / Biggin, P.C. / Mayer, M.L. #1: Journal: Neuron / Year: 2007 Title: Structure and mechanism of kainate receptor modulation by anions. Authors: Plested, A.J. / Mayer, M.L. #2: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c34.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c34.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c34_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 3c34_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 3c34_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 3c34_validation.cif.gz | 40.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c34 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c34 | HTTPS FTP |
-Related structure data
Related structure data | 3c31SC 3c32C 3c33C 3c35C 3c36C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29253.566 Da / Num. of mol.: 2 / Fragment: Residues 446-821 Source method: isolated from a genetically manipulated source Details: REMARK 999 THE FIRST TWO RESIDUES OF THE SEQUENCE ARE REMARK 999 VECTOR ENCODED . GLUR5 RESIDUES 446-559 AND REMARK 999 682-821 ARE LINKED VIA GLY-THR DIPEPTIDE . Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK1, GLUR5 / Plasmid: Modified pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P22756 |
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-Non-polymers , 5 types, 572 molecules
#2: Chemical | ChemComp-RB / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682-821 ARE ...THE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682-821 ARE LINKED VIA GLY-THR DIPEPTIDE. |
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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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 4000, 125 mM RbCl, 175 mM Rb2(SO4), 100 mM Rb cacodylate, 4 mM Kainic acid, pH 6.0, 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: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→40 Å / Num. all: 54555 / Num. obs: 54555 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 6 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 5.22 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3C31 Resolution: 1.82→38.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.162 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.119 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→38.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.87 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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