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- PDB-4oo9: Structure of the human class C GPCR metabotropic glutamate recept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oo9 | ||||||
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Title | Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator mavoglurant | ||||||
![]() | Metabotropic glutamate receptor 5, Lysozyme, Metabotropic glutamate receptor 5 chimera | ||||||
![]() | MEMBRANE PROTEIN / 7TM / receptor / G-protein / cysteine-S-acetamide | ||||||
Function / homology | ![]() A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection ...A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / : / viral release from host cell by cytolysis / regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / protein tyrosine kinase binding / dendritic shaft / learning / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / synapse organization / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (q) signalling events / chemical synaptic transmission / host cell cytoplasm / positive regulation of MAPK cascade / dendritic spine / learning or memory / defense response to bacterium / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. ...Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. / Weir, M. / Wiggin, G.R. / Marshall, F.H. | ||||||
![]() | ![]() Title: Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain. Authors: Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. / Weir, M. / Wiggin, G.R. / Marshall, F.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177 KB | Display | ![]() |
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PDB format | ![]() | 138.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u19S ![]() 3emlS ![]() 3uonS ![]() 3v2yS ![]() 4dajS ![]() 4djhS ![]() 4dklS ![]() 4ea3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49916.641 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GRM5, GPRC1E, MGLUR5, E / Plasmid: FastBac / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-OLA / #3: Chemical | ChemComp-2U8 / | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Sequence details | PROTEIN IS A CHIMERA COMPRISING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293.1 K / Method: lipidic cubic phase / pH: 6.8 Details: 24-34% v/v PEG400, 0.2 M ammonium phosphate dibasic, 0.1 M MES, pH 6.8, LIPIDIC CUBIC PHASE, temperature 293.1K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→80.955 Å / Num. all: 14800 / Num. obs: 14800 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.8 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19 Resolution: 2.6→29.74 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 30.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.74 Å
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Refine LS restraints |
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LS refinement shell |
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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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