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- PDB-5xra: Crystal structure of the human CB1 in complex with agonist AM11542 -

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Basic information

Entry
Database: PDB / ID: 5xra
TitleCrystal structure of the human CB1 in complex with agonist AM11542
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 / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor 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 ...cannabinoid signaling pathway / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor 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 / FMN binding / actin cytoskeleton / glucose homeostasis / growth cone / presynaptic membrane / G alpha (i) signalling events / mitochondrial outer membrane / electron transfer activity / 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 / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. ...Cannabinoid receptor type 1 / Cannabinoid receptor family / Flavodoxin, short chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8D3 / CHOLESTEROL / FLAVIN MONONUCLEOTIDE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Flavodoxin / Cannabinoid receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 8, 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 / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _software.version
Revision 1.4Oct 18, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)51,3049
Polymers48,6281
Non-polymers2,6778
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.050, 75.870, 138.900
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
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 / Production host: Homo sapiens (human) / References: UniProt: P21554, UniProt: P00323

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Non-polymers , 6 types, 8 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-8D3 / (6aR,10aR)-3-(8-bromanyl-2-methyl-octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol


Mass: 449.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C25H37BrO2
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O

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Details

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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M sodium cacodylate trihydrate pH 6.4, 300-350 mM C4H4KNaO6, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→37.91 Å / Num. obs: 16685 / % possible obs: 93.5 % / Redundancy: 6.1 % / Net I/σ(I): 10.41
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.07 / % possible all: 90.03

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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: 2.8→37.91 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.49
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.
RfactorNum. reflection% reflection
Rfree0.2519 805 4.83 %
Rwork0.2341 --
obs0.235 16669 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 150 0 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033539
X-RAY DIFFRACTIONf_angle_d0.7324811
X-RAY DIFFRACTIONf_dihedral_angle_d17.2712033
X-RAY DIFFRACTIONf_chiral_restr0.04562
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97540.40271050.3922504X-RAY DIFFRACTION90
2.9754-3.20510.38561280.34112530X-RAY DIFFRACTION91
3.2051-3.52740.29531410.28342615X-RAY DIFFRACTION94
3.5274-4.03730.26391410.24832670X-RAY DIFFRACTION95
4.0373-5.08470.26131400.19982712X-RAY DIFFRACTION95
5.0847-37.91640.19731500.19732833X-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)
14.33230.1288-0.24321.39210.49632.63350.04290.3638-0.2032-0.15740.0364-0.1851-0.0318-0.1245-0.08750.49550.0257-0.02310.3907-0.06340.4658-45.7418-153.3025304.144
26.7869-1.97510.3855.0614-1.64836.1613-0.0179-0.21640.30330.36320.0139-0.1697-0.3488-0.09990.0210.6676-0.01970.01250.51140.020.8596-43.2031-118.0939257.7939
32.04242.42531.04357.04381.17632.1106-0.14830.07020.03380.13350.14640.1466-0.10370.2170.0220.51290.04870.12020.698-0.05930.7613-36.6663-150.5189299.6294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 306 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1002 through 1148 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 414 )

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