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- PDB-5u09: High-resolution crystal structure of the human CB1 cannabinoid re... -

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Basic information

Entry
Database: PDB / ID: 5u09
TitleHigh-resolution crystal structure of the human CB1 cannabinoid receptor
ComponentsCannabinoid receptor 1,GlgA glycogen synthase
KeywordsMEMBRANE PROTEIN / helix
Function / homology
Function and homology information


cannabinoid signaling pathway / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / regulation of presynaptic cytosolic calcium ion concentration / Class A/1 (Rhodopsin-like receptors) / axonal fasciculation / regulation of metabolic process / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity ...cannabinoid signaling pathway / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / regulation of presynaptic cytosolic calcium ion concentration / Class A/1 (Rhodopsin-like receptors) / axonal fasciculation / regulation of metabolic process / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity / GABA-ergic synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / glucose homeostasis / actin cytoskeleton / presynaptic membrane / growth cone / G alpha (i) signalling events / mitochondrial outer membrane / membrane raft / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm
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-7DY / 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: 2.6 Å
AuthorsShao, Z.H. / Yin, J. / Rosenbaum, D.
CitationJournal: 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
DepositionNov 23, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionDec 7, 2016ID: 5TJV
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 4, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,25115
Polymers57,3951
Non-polymers1,85514
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.652, 80.381, 81.178
Angle α, β, γ (deg.)90.000, 91.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


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
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-7DY / N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide


Mass: 515.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25ClF3N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.6-2.695.11.4110.69196.8
2.69-2.85.21.1210.717197
2.8-2.935.70.9840.815197.1
2.93-3.085.60.740.885197.4
3.08-3.285.60.520.937198
3.28-3.535.30.3180.966197.5
3.53-3.885.10.2150.975196.7
3.88-4.455.50.1440.984196.8
4.45-5.65.30.1160.977197.2
5.6-505.30.070.995194.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V2Y

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 612 5.2 %RANDOM
Rwork0.1803 ---
obs0.1832 11084 57.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.65 Å2 / Biso mean: 44.12 Å2 / Biso min: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1-6.05 Å2-0 Å21.27 Å2
2---2.83 Å2-0 Å2
3----3.3 Å2
Refinement stepCycle: final / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 119 62 3943
Biso mean--58.54 31.58 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193976
X-RAY DIFFRACTIONr_bond_other_d0.0010.023962
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9935348
X-RAY DIFFRACTIONr_angle_other_deg0.6433.0029081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6545475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48822.5152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96615699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.711526
X-RAY DIFFRACTIONr_chiral_restr0.2490.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024252
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02912
X-RAY DIFFRACTIONr_mcbond_it4.5494.0031909
X-RAY DIFFRACTIONr_mcbond_other4.54741908
X-RAY DIFFRACTIONr_mcangle_it6.8866.0012381
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 3 -
Rwork0.253 48 -
all-51 -
obs--3.42 %

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