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Yorodumi- PDB-5u09: High-resolution crystal structure of the human CB1 cannabinoid re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u09 | |||||||||
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Title | High-resolution crystal structure of the human CB1 cannabinoid receptor | |||||||||
Components | Cannabinoid receptor 1,GlgA glycogen synthase | |||||||||
Keywords | MEMBRANE PROTEIN / helix | |||||||||
Function / homology | Function and homology information cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / negative regulation of mast cell activation / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / glycogen (starch) synthase activity / negative regulation of fatty acid beta-oxidation / negative regulation of dopamine secretion / positive regulation of acute inflammatory response to antigenic stimulus ...cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / negative regulation of mast cell activation / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / glycogen (starch) synthase activity / negative regulation of fatty acid beta-oxidation / negative regulation of dopamine secretion / positive regulation of acute inflammatory response to antigenic stimulus / regulation of feeding behavior / negative regulation of serotonin secretion / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of action potential / Class A/1 (Rhodopsin-like receptors) / positive regulation of blood pressure / regulation of metabolic process / positive regulation of fever generation / axonal fasciculation / regulation of synaptic transmission, GABAergic / regulation of insulin secretion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / GABA-ergic synapse / maternal process involved in female pregnancy / regulation of synaptic transmission, glutamatergic / negative regulation of blood pressure / response to nutrient / response to cocaine / G protein-coupled receptor activity / response to nicotine / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / memory / positive regulation of neuron projection development / actin cytoskeleton / glucose homeostasis / presynaptic membrane / G alpha (i) signalling events / growth cone / spermatogenesis / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / membrane raft / positive regulation of apoptotic process / nucleotide binding / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Pyrococcus abyssi (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Shao, Z.H. / Yin, J. / Rosenbaum, D. | |||||||||
Citation | Journal: Nature / Year: 2016 Title: High-resolution crystal structure of the human CB1 cannabinoid receptor. Authors: Shao, Z. / Yin, J. / Chapman, K. / Grzemska, M. / Clark, L. / Wang, J. / Rosenbaum, D.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u09.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u09.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 5u09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/5u09 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u09 | HTTPS FTP |
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-Related structure data
Related structure data | 3v2yS 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
#1: Protein | Mass: 57395.387 Da / Num. of mol.: 1 Fragment: P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413 Mutation: T210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Gene: CNR1, CNR, PAB2292 / Plasmid: PFASTbac / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P21554, UniProt: Q9V2J8 | ||||||
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#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-7DY / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50.01 Å / Num. obs: 19781 / % possible obs: 96.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.194 / Net I/av σ(I): 7.432 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V2Y Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.88 / SU B: 10.364 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AS PER THE AUTHORS THE NUMBER OF OBSERVED REFLECTIONS USED FOR REFINEMENT IS LOW DUE TO ANISOTROPIC TRUNCATION OF THE DATA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.65 Å2 / Biso mean: 44.12 Å2 / Biso min: 7.02 Å2
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Refinement step | Cycle: final / Resolution: 2.6→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.665 Å / Total num. of bins used: 20
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