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- PDB-6kqi: Structure of an allosteric modulator bound to the CB1 cannabinoid... -

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Basic information

Entry
Database: PDB / ID: 6kqi
TitleStructure of an allosteric modulator bound to the CB1 cannabinoid receptor
ComponentsCannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1
KeywordsCELL CYCLE / 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 / 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
Cannabinoid receptor type 1 / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Cannabinoid receptor family / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Cannabinoid receptor type 1 / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Cannabinoid receptor family / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-9GF / Chem-9GL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Cannabinoid receptor 1 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.245 Å
AuthorsShao, Z.H. / Yan, W.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structure of an allosteric modulator bound to the CB1 cannabinoid receptor.
Authors: Shao, Z. / Yan, W. / Chapman, K. / Ramesh, K. / Ferrell, A.J. / Yin, J. / Wang, X. / Xu, Q. / Rosenbaum, D.M.
History
DepositionAug 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 28, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,38711
Polymers55,5461
Non-polymers2,84210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint18 kcal/mol
Surface area23580 Å2
Unit cell
Length a, b, c (Å)41.342, 167.940, 41.526
Angle α, β, γ (deg.)90.000, 91.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1 / CB1 / CANN6 / Glycogen synthase


Mass: 55545.547 Da / Num. of mol.: 1 / Fragment: C1 / Mutation: S203K,T210A,E273K,T283V,R340E
Source method: isolated from a genetically manipulated source
Details: The fusion protein of UNP residues 94-301 (Cannabinoid receptor 1), UNP residues 218-413 (GlgA glycogen synthase), and UNP residues 333-413 (Cannabinoid receptor 1)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: CNR1, CNR, PAB2292 / Plasmid: PFASTbac / Strain: GE5 / Orsay / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21554, UniProt: Q9V2J8

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-9GF / 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol


Mass: 376.573 Da / Num. of mol.: 1 / Fragment: Tar / Source method: obtained synthetically / Formula: C24H40O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9GL / 5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide


Mass: 409.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN3O / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 33% PEG 400, 100mM Sodium Cacodylate pH 6.0, 100mM Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.245→50 Å / Num. obs: 8201 / % possible obs: 92.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 72.36 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.108 / Rrim(I) all: 0.222 / Χ2: 0.824 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.373.21.1558300.4370.6771.350.83494.7
3.37-3.53.50.9668070.5240.5441.1180.81893.1
3.5-3.663.40.5868440.7020.3410.6830.82594.2
3.66-3.853.50.4098560.8450.2370.4760.83896.2
3.85-4.093.60.3028320.8750.1660.3470.96593.7
4.09-4.413.50.2138150.9430.1190.2460.91894.1
4.41-4.853.30.178130.9490.0970.1970.95891.2
4.85-5.563.40.1448270.9710.080.1660.76994.4
5.56-73.60.1498460.9380.0820.1710.66893.2
7-503.50.0877310.9740.0480.1010.64580.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U09

5u09


Resolution: 3.245→33.345 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 34.69
RfactorNum. reflection% reflection
Rfree0.312 763 9.88 %
Rwork0.2291 --
obs0.2376 7721 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.79 Å2 / Biso mean: 62.1596 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.245→33.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 145 0 3828
Biso mean--60.91 --
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033893
X-RAY DIFFRACTIONf_angle_d0.6035243
X-RAY DIFFRACTIONf_chiral_restr0.04609
X-RAY DIFFRACTIONf_plane_restr0.004632
X-RAY DIFFRACTIONf_dihedral_angle_d8.542333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2454-3.49570.38071200.295113370
3.4957-3.8470.36481670.2587140388
3.847-4.40260.31951550.2316149593
4.4026-5.54270.31041680.208149392
5.5427-33.3450.26031530.212143487

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