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- PDB-5u09: High-resolution crystal structure of the human CB1 cannabinoid re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u09 | |||||||||
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Title | High-resolution crystal structure of the human CB1 cannabinoid receptor | |||||||||
![]() | Cannabinoid receptor 1,GlgA glycogen synthase | |||||||||
![]() | MEMBRANE PROTEIN / helix | |||||||||
Function / homology | ![]() 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 / positive regulation of fever generation / regulation of metabolic process / axonal fasciculation / glycogen biosynthetic process / 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 / positive regulation of apoptotic process / membrane raft / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shao, Z.H. / Yin, J. / Rosenbaum, D. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.1 KB | Display | ![]() |
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Full document | ![]() | 775.7 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v2yS 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
#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.) ![]() ![]() ![]() Gene: CNR1, CNR, PAB2292 / Plasmid: PFASTbac / Strain: GE5 / Orsay / Production host: ![]() ![]() | ||||||
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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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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