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- PDB-5xr8: Crystal structure of the human CB1 in complex with agonist AM841 -

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Basic information

Entry
Database: PDB / ID: 5xr8
TitleCrystal structure of the human CB1 in complex with agonist AM841
ComponentsCannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1
KeywordsSIGNALING PROTEIN / Membrane protein / human G protein-coupled receptor / stabilizing agonists / lipidic cubic phase
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 presynaptic cytosolic calcium ion concentration ...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 presynaptic cytosolic calcium ion concentration / regulation of feeding behavior / negative regulation of serotonin secretion / 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 / 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 / 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 / positive regulation of neuron projection development / memory / 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-8D0 / CHOLESTEROL / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Flavodoxin / Cannabinoid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHua, 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.
CitationJournal: Nature / Year: 2017
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
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4Oct 18, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.0Jan 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.title / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.selection_details / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _refine.details / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Nov 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

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)50,0225
Polymers48,6281
Non-polymers1,3954
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.830, 73.610, 139.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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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: 48627.582 Da / Num. of mol.: 1
Fragment: UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,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.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Gene: CNR1, CNR, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21554, UniProt: P00323

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Non-polymers , 5 types, 5 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-8D0 / (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol


Mass: 445.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39NO3S
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.2
Details: 0.1 M sodium cacodylate trihydrate pH 6.2, 120 mM C6H5Na3O7, 30% PEG400 and 100 mM Glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→49.48 Å / Num. obs: 13367 / % possible obs: 88.18 % / Redundancy: 6.3 % / Net I/σ(I): 11.06
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.97 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TGZ

5tgz


Resolution: 2.95→49.48 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.26
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; DUE TO LACK OF ...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; DUE TO LACK OF DENSITIES, LAST TWO C AND S ATOMS IN THE TAIL OF THE LIGAND 8D0 HAS BEEN DELETED DURING THE FINAL REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2742 618 4.64 %
Rwork0.2548 --
obs0.2557 13329 88.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 95 1 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023491
X-RAY DIFFRACTIONf_angle_d0.4844764
X-RAY DIFFRACTIONf_dihedral_angle_d15.5032016
X-RAY DIFFRACTIONf_chiral_restr0.036561
X-RAY DIFFRACTIONf_plane_restr0.003600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.24680.40941270.38582770X-RAY DIFFRACTION78
3.2468-3.71650.39981590.31973046X-RAY DIFFRACTION86
3.7165-4.68190.26711550.26653282X-RAY DIFFRACTION92
4.6819-49.48660.2421770.22493613X-RAY DIFFRACTION96
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)
15.24211.01270.3311.14920.35752.96240.24690.34850.02820.00830.10190.30890.1342-0.2645-0.3070.48160.067-0.04210.3626-0.0210.764-46.5828-149.0927305.7149
28.3074-4.14742.73377.224-4.60725.4565-0.4097-0.13390.35081.05890.0256-0.4847-0.4268-0.16130.43330.8387-0.040.0550.6905-0.00711.5988-35.983-118.941259.68
32.7720.53751.32162.10892.96284.3409-0.20970.06590.27040.3455-0.11911.0514-0.6220.18660.30590.7203-0.02550.18570.625-0.02450.889-41.886-126.754276.328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 306 )
2X-RAY DIFFRACTION2chain 'A' and (resid 307 through 335 )
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 536 )

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