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- PDB-5tgz: Crystal Structure of the Human Cannabinoid Receptor CB1 -

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Basic information

Entry
Database: PDB / ID: 5tgz
TitleCrystal Structure of the Human Cannabinoid Receptor CB1
ComponentsCannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1
KeywordsSIGNALING PROTEIN / Membrane protein / G protein-coupled receptor / human cannabinoid receptor CB1 / marijuana / stabilizing antagonist AM6538 / lipidic cubic phase / CB1-Flavodoxin chimera
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 / 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 / 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 domain / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Flavodoxin-like / Flavodoxin ...Cannabinoid receptor type 1 / Cannabinoid receptor family / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Chem-ZDG / Flavodoxin / Cannabinoid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHua, T. / Vemuri, K. / Pu, M. / Qu, L. / Han, G.W. / Wu, Y. / Zhao, S. / Shui, W. / Li, S. / Korde, A. ...Hua, T. / Vemuri, K. / Pu, M. / Qu, L. / Han, G.W. / Wu, Y. / Zhao, S. / Shui, W. / Li, S. / Korde, A. / Laprairie, R.B. / Stahl, E.L. / Ho, J.H. / Zvonok, N. / Zhou, H. / Kufareva, I. / Wu, B. / Zhao, Q. / Hanson, M.A. / Bohn, L.M. / Makriyannis, A. / Stevens, R.C. / Liu, Z.J.
CitationJournal: Cell / Year: 2016
Title: Crystal Structure of the Human Cannabinoid Receptor CB1.
Authors: Hua, T. / Vemuri, K. / Pu, M. / Qu, L. / Han, G.W. / Wu, Y. / Zhao, S. / Shui, W. / Li, S. / Korde, A. / Laprairie, R.B. / Stahl, E.L. / Ho, J.H. / Zvonok, N. / Zhou, H. / Kufareva, I. / Wu, ...Authors: Hua, T. / Vemuri, K. / Pu, M. / Qu, L. / Han, G.W. / Wu, Y. / Zhao, S. / Shui, W. / Li, S. / Korde, A. / Laprairie, R.B. / Stahl, E.L. / Ho, J.H. / Zvonok, N. / Zhou, H. / Kufareva, I. / Wu, B. / Zhao, Q. / Hanson, M.A. / Bohn, L.M. / Makriyannis, A. / Stevens, R.C. / Liu, Z.J.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Structure summary
Category: audit_author / diffrn_source / pdbx_struct_oper_list
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6468
Polymers50,3371
Non-polymers2,3097
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.560, 52.630, 143.630
Angle α, β, γ (deg.)90.00, 111.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1 / CB1 / CANN6


Mass: 50337.375 Da / Num. of mol.: 1
Fragment: UNP RESIDUES 99-306,UNP RESIDUES 2-148,UNP RESIDUES 332-414
Mutation: T210A, E273K, T283V,P1002A, Y1098W,R340E
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Cannabinoid receptor 1 (RESIDUES 99-306), Flavodoxin (RESIDUES 1002-1148), and Cannabinoid receptor 1 (RESIDUES 332-414)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris (bacteria)
Gene: CNR1, CNR, DVU_2680 / Plasmid: pTT5 / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Cell (production host): HEK293F / Cell line (production host): FreeStyle 293-F (HEK-293F) / Production host: Homo sapiens (human) / References: UniProt: P21554, UniProt: P00323

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Non-polymers , 6 types, 16 molecules

#2: Chemical ChemComp-ZDG / 4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl nitrate


Mass: 542.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25Cl2N5O4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE NITRATE GROUP OF LIGAND ZDG BOUND TO THE CB1 STRUCTURE HAS NOT BEEN MODELED DUE TO LACK OF ...THE NITRATE GROUP OF LIGAND ZDG BOUND TO THE CB1 STRUCTURE HAS NOT BEEN MODELED DUE TO LACK OF ELECTRON DENSITY ON THE NITRATE GROUP.

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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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M HEPES pH 7.0-7.4, 100mM (NH4)2HPO4, 25%-32% PEG 400, 2-20 mM Ethylenediaminetetraacetic acid disodium salt dehydrate (EDTA)
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.05 Å / Num. obs: 19837 / % possible obs: 97.4 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.1
Reflection shellHighest resolution: 2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.44 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIXdev_2289refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z34, 1I1O

4z34

1i1o


Resolution: 2.8→47.045 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.73
RfactorNum. reflection% reflection
Rfree0.2376 985 4.97 %
Rwork0.2065 --
obs0.2081 19827 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 126 9 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043620
X-RAY DIFFRACTIONf_angle_d0.6384904
X-RAY DIFFRACTIONf_dihedral_angle_d20.3161282
X-RAY DIFFRACTIONf_chiral_restr0.04558
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.31161280.29442559X-RAY DIFFRACTION94
2.9476-3.13230.31611360.26712603X-RAY DIFFRACTION95
3.1323-3.37410.2491280.23442671X-RAY DIFFRACTION97
3.3741-3.71350.25621500.21792677X-RAY DIFFRACTION98
3.7135-4.25050.22431520.20162744X-RAY DIFFRACTION99
4.2505-5.3540.22331380.18042765X-RAY DIFFRACTION99
5.354-47.05170.22071530.19292823X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90320.24670.58291.23861.28532.4083-0.1308-0.1669-0.070.29790.0936-0.0950.01030.2053-0.00950.5212-0.0054-0.03270.45520.13770.479837.235423.2794296.3046
22.6694-4.47871.04418.3108-1.6650.41760.02760.03610.0855-0.06150.0091-0.20880.06740.0866-0.02521.7067-0.0933-0.01361.2873-0.10091.205443.897627.5518318.1843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resid 99:306) or (resid 1002:1148) or (resid 332:412))
2X-RAY DIFFRACTION2chain 'A' and (resid 2001:2001)

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