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Yorodumi- PDB-2e4z: Crystal structure of the ligand-binding region of the group III m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e4z | ||||||
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Title | Crystal structure of the ligand-binding region of the group III metabotropic glutamate receptor | ||||||
Components | Metabotropic glutamate receptor 7 | ||||||
Keywords | SIGNALING PROTEIN / G-protein-coupled receptor / neuron / central nerve system | ||||||
Function / homology | Function and homology information group III metabotropic glutamate receptor activity / : / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / negative regulation of glutamate secretion / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / serine binding ...group III metabotropic glutamate receptor activity / : / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / negative regulation of glutamate secretion / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / serine binding / short-term memory / conditioned taste aversion / G protein-coupled glutamate receptor signaling pathway / nervous system process / glutamate receptor activity / G alpha (i) signalling events / glutamate binding / regulation of synaptic vesicle exocytosis / adult behavior / axon development / transmission of nerve impulse / plasma membrane => GO:0005886 / presynaptic active zone / associative learning / calcium channel regulator activity / asymmetric synapse / GABA-ergic synapse / voltage-gated calcium channel activity / behavioral fear response / multicellular organismal response to stress / axon terminus / rough endoplasmic reticulum / regulation of synaptic transmission, glutamatergic / dendritic shaft / PDZ domain binding / sensory perception of sound / terminal bouton / memory / calcium-dependent protein binding / presynaptic membrane / cell cortex / chemical synaptic transmission / postsynaptic membrane / negative regulation of neuron apoptotic process / receptor complex / membrane => GO:0016020 / learning or memory / calmodulin binding / protein dimerization activity / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / cell surface / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Muto, T. / Tsuchiya, D. / Morikawa, K. / Jingami, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structures of the extracellular regions of the group II/III metabotropic glutamate receptors Authors: Muto, T. / Tsuchiya, D. / Morikawa, K. / Jingami, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e4z.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e4z.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e4z_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
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Full document | 2e4z_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 2e4z_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2e4z_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/2e4z ftp://data.pdbj.org/pub/pdb/validation_reports/e4/2e4z | HTTPS FTP |
-Related structure data
Related structure data | 2e4uC 2e4vC 2e4wC 2e4xC 2e4yC 1ewkS 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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Details | The second part of the biological assembly is generated by the two fold axis: X-Y,-Y,-1/3-Z |
-Components
#1: Protein | Mass: 56030.871 Da / Num. of mol.: 1 / Fragment: ligand-binding region, residues 33-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35400 |
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#2: Chemical | ChemComp-MES / |
-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: 51.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.02M Citrate, 0.08M MES, 0.01M Glutamate, 2.2M ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2004 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→100 Å / Num. all: 8887 / Num. obs: 8887 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.112 / Rsym value: 0.106 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3.3→3.48 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EWK Resolution: 3.3→12 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.823 / SU B: 33.152 / SU ML: 0.579 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R Free: 0.702 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.703 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.379 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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