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- PDB-7v3z: Structure of cannabinoid receptor type 1(CB1) -

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Basic information

Entry
Database: PDB / ID: 7v3z
TitleStructure of cannabinoid receptor type 1(CB1)
Componentsfusion protein of Cannabinoid receptor 1 and Flavodoxin
KeywordsMEMBRANE PROTEIN / Activation
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 / 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 / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of insulin secretion / maternal process involved in female pregnancy / GABA-ergic synapse / regulation of synaptic transmission, glutamatergic / negative regulation of blood pressure / response to nutrient / response to cocaine / response to nicotine / G protein-coupled receptor activity / 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 / FMN binding / presynaptic membrane / G alpha (i) signalling events / growth cone / 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
Cannabinoid receptor type 1 / Cannabinoid receptor family / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Serpentine type 7TM GPCR chemoreceptor Srsx ...Cannabinoid receptor type 1 / Cannabinoid receptor family / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Serpentine type 7TM GPCR chemoreceptor Srsx / Flavoprotein-like superfamily / 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 / CHOLESTEROL / FLAVIN MONONUCLEOTIDE / Flavodoxin / Cannabinoid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsLiu, Z.J. / Shen, L. / Hua, T. / Yao, D.Q. / Wu, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953202, 21837005, 31670733,31870744 China
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: A Genetically Encoded F-19 NMR Probe Reveals the Allosteric Modulation Mechanism of Cannabinoid Receptor 1.
Authors: Wang, X. / Liu, D. / Shen, L. / Li, F. / Li, Y. / Yang, L. / Xu, T. / Tao, H. / Yao, D. / Wu, L. / Hirata, K. / Bohn, L.M. / Makriyannis, A. / Liu, X. / Hua, T. / Liu, Z.J. / Wang, J.
History
DepositionAug 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein of Cannabinoid receptor 1 and Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8224
Polymers48,6031
Non-polymers1,2203
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.810, 75.350, 138.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein fusion protein of Cannabinoid receptor 1 and Flavodoxin / / CB-R / CB1 / CANN6


Mass: 48602.590 Da / Num. of mol.: 1 / Mutation: H154L,T210A,E273K,T283V,Y1098W,R340E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: CNR1, CNR, DVU_2680 / Strain: Hildenborough
Production host: Mammalian expression vector Flag-EGFP-MCS-pcDNA3.1 (others)
References: UniProt: P21554, UniProt: P00323
#2: Chemical ChemComp-9GF / 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol / CP 55,940


Mass: 376.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7.2
Details: 30% PEG400, 100 mM HEPES sodium pH 7.2, 80-100mM sodium citrate tribasic dihydrate
PH range: 6.8-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→24.78 Å / Num. obs: 11228 / % possible obs: 99.9 % / Redundancy: 74.9 % / Biso Wilson estimate: 151.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.54 / Rrim(I) all: 0.544 / Χ2: 1.219 / Net I/σ(I): 11.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRmerge(I) obs
3.27-3.4774.9250.9717920.58114.281100
3.47-3.7176.8952.1116600.844.0241003.998
3.71-482.2243.815300.9432.2791002.265
4-4.3980.5627.8614830.9771.1221001.115
4.39-4.976.49513.7412860.9910.6191000.615
4.9-5.6682.1516.1711850.9920.4891000.486
5.66-6.9476.16317.7210100.9940.4341000.431
6.94-9.8175.70237.767980.9980.2141000.213
9.81-24.7866.89949.414840.9990.16198.40.159

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHENIXmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XRA

5xra


Resolution: 3.29→24.78 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
RfactorNum. reflection% reflectionSelection details
Rfree0.276 539 4.92 %RANDOM
Rwork0.215 ---
obs0.218 10955 100 %-
Displacement parametersBiso max: 235.9 Å2 / Biso mean: 142.32 Å2 / Biso min: 99.27 Å2
Baniso -1Baniso -2Baniso -3
1--2.9063 Å20 Å20 Å2
2--30.2755 Å20 Å2
3----27.3692 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 3.29→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 86 0 3398
Biso mean--120.04 --
Num. residues----431
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1137SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes563HARMONIC5
X-RAY DIFFRACTIONt_it3479HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion466SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4211SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3479HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4747HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.12
X-RAY DIFFRACTIONt_other_torsion21.78
LS refinement shellResolution: 3.29→3.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.3805 13 3.08 %
Rwork0.2295 409 -
all0.2339 422 -
obs--100 %

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