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Yorodumi- PDB-3kfm: Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kfm | ||||||
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Title | Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate | ||||||
Components | Glutamate receptor 4 | ||||||
Keywords | TRANSPORT PROTEIN / GluA4 / AMPA receptor / ligand-gated ion channel / ligand-binding domain / L651V / kainate / Alternative splicing / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport | ||||||
Function / homology | Function and homology information Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / 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 / chemical synaptic transmission / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gill, A. / Madden, D.R. | ||||||
Citation | Journal: J.Neurosci. / Year: 2010 Title: Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors. Authors: Birdsey-Benson, A. / Gill, A. / Henderson, L.P. / Madden, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kfm.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kfm.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfm ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfm | HTTPS FTP |
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-Related structure data
Related structure data | 3keiC 3en3S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28723.168 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Mutation: L134V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: Glur4, Gria4 / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): XJb(DE3) / References: UniProt: P19493 |
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#2: Chemical | ChemComp-KAI / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE MATCHES TO ISOFORM 2 OF UNIPROT ENTRY P19493 (IDENTIFIER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | Temperature: 291 K / pH: 5 Details: 18% PEG 8000, 0.1M Na-Acetate, 0.2M Ammonium Sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2006 |
Radiation | Monochromator: FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 13431 / % possible obs: 99.3 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.25 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EN3 Resolution: 2.2→19.95 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 13.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å / Num. reflection Rfree: 48 |