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- PDB-5xra: Crystal structure of the human CB1 in complex with agonist AM11542 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xra | ||||||
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Title | Crystal structure of the human CB1 in complex with agonist AM11542 | ||||||
![]() | Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1 | ||||||
![]() | SIGNALING PROTEIN / Membrane protein / human G protein-coupled receptor / stabilizing agonists / lipidic cubic phase | ||||||
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 / 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 ...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 / 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 / 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 / FMN binding / glucose homeostasis / presynaptic membrane / growth cone / G alpha (i) signalling events / spermatogenesis / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / positive regulation of apoptotic process / membrane raft / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hua, T. / Vemuri, K. / Nikas, P.S. / Laprairie, R.B. / Wu, Y. / Qu, L. / Pu, M. / Korde, A. / Shan, J. / Ho, J.H. ...Hua, T. / Vemuri, K. / Nikas, P.S. / Laprairie, R.B. / Wu, Y. / Qu, L. / Pu, M. / Korde, A. / Shan, J. / Ho, J.H. / Han, G.W. / Ding, K. / Li, X. / Liu, H. / Hanson, M.A. / Zhao, S. / Bohn, L.M. / Makriyannis, A. / Stevens, R.C. / Liu, Z.J. | ||||||
![]() | ![]() Title: Crystal structures of agonist-bound human cannabinoid receptor CB1 Authors: Hua, T. / Vemuri, K. / Nikas, S.P. / Laprairie, R.B. / Wu, Y. / Qu, L. / Pu, M. / Korde, A. / Jiang, S. / Ho, J.H. / Han, G.W. / Ding, K. / Li, X. / Liu, H. / Hanson, M.A. / Zhao, S. / Bohn, ...Authors: Hua, T. / Vemuri, K. / Nikas, S.P. / Laprairie, R.B. / Wu, Y. / Qu, L. / Pu, M. / Korde, A. / Jiang, S. / Ho, J.H. / Han, G.W. / Ding, K. / Li, X. / Liu, H. / Hanson, M.A. / Zhao, S. / Bohn, L.M. / Makriyannis, A. / Stevens, R.C. / Liu, Z.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.4 KB | Display | ![]() |
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PDB format | ![]() | 149.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xr8C ![]() 5tgzS S: Starting model for refinement C: citing same article ( |
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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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48627.582 Da / Num. of mol.: 1 Fragment: UNP residues 99-306,UNP residues 3-148,UNP residues 332-414 Mutation: T210A, E273K, T283V,Y1098W,R340E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CNR1, CNR, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Production host: ![]() |
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-Non-polymers , 6 types, 8 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/8D3.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/8D3.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CLR.gif)
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | ChemComp-8D3 / ( | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-CLR / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.1 M sodium cacodylate trihydrate pH 6.4, 300-350 mM C4H4KNaO6, 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.91 Å / Num. obs: 16685 / % possible obs: 93.5 % / Redundancy: 6.1 % / Net I/σ(I): 10.41 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.07 / % possible all: 90.03 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TGZ Resolution: 2.8→37.91 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.49 Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED AT THE END OF THE SIDE CHAIN OF SER152, WHICH MIGHT BE PHOSPHORYLATION BUT NOT CHEMICALLY CONFIRMED YET. THEY HAVE NOT BEEN MODELLED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.91 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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