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Yorodumi- PDB-3fvo: Crystal structure of the human glutamate receptor, GluR5, ligand-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fvo | ||||||
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Title | Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1 | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / glutamate receptor / ligand-binding domain / 8-epi-neodysiherbaine | ||||||
Function / homology | Function and homology information Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / nervous system development / chemical synaptic transmission / intracellular membrane-bounded organelle / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Unno, M. / Sasaki, M. / Ikeda-Saito, M. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Human GluR5 Ligand-Binding Core in Complexes with Novel Marine-Derived Toxins, Dysiherbaine and Neodysiherbaine A, and Their Analogues Authors: Unno, M. / Shinohara, M. / Takayama, K. / Teruya, K. / Doh-ura, K. / Sakai, R. / Sasaki, M. / Ikeda-Saito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fvo.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fvo.ent.gz | 182 KB | Display | PDB format |
PDBx/mmJSON format | 3fvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fvo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3fvo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3fvo_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3fvo_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/3fvo ftp://data.pdbj.org/pub/pdb/validation_reports/fv/3fvo | HTTPS FTP |
-Related structure data
Related structure data | 2zntS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29093.441 Da / Num. of mol.: 2 Fragment: ligand-binding domain, UNP residues 445-559, 682-820 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus: GRIK1, GLUR5 / Plasmid: pCold-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39086 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 35% PEG3350, 0.3M LiSO4, 5mM 8-epi-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 79930 / % possible obs: 96.9 % / Redundancy: 3.6 % / Rsym value: 0.05 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5.11 / Num. unique all: 7800 / Rsym value: 0.135 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZNT Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.101 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.926 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 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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