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- PDB-2b0y: Solution Structure of a peptide mimetic of the fourth cytoplasmic... -

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Basic information

Entry
Database: PDB / ID: 2b0y
TitleSolution Structure of a peptide mimetic of the fourth cytoplasmic loop of the G-protein coupled CB1 cannabinoid receptor
ComponentsCannabinoid receptor 1
KeywordsCELL ADHESION / cell surface receptors / G-protein coupled receptors / CB1 cannabinoid receptors / GTP-binding proteins / two-dimensional proton nuclear magnetic resonance (2D 1H-NMR) spectroscopy / DQF-COSY / TOCSY / NOESY / ROESY / sodium dodecylsulfate (SDS) micelles / signal transduction mechanisms
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 / glucose homeostasis / presynaptic membrane / G alpha (i) signalling events / growth cone / spermatogenesis / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / 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 / 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
Cannabinoid receptor 1
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing(DYANA)
AuthorsGrace, C.R. / Cowsik, S.M. / Shim, J.Y. / Welsh, W.J. / Howlett, A.C.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Unique helical conformation of the fourth cytoplasmic loop of the CB1 cannabinoid receptor in a negatively charged environment.
Authors: Grace, C.R. / Cowsik, S.M. / Shim, J.Y. / Welsh, W.J. / Howlett, A.C.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cannabinoid receptor 1


Theoretical massNumber of molelcules
Total (without water)2,0561
Polymers2,0561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Cannabinoid receptor 1 / CB1 / CB-R / CANN6


Mass: 2056.330 Da / Num. of mol.: 1
Fragment: Fragment of the C-terminal juxtramembrane region of CB1 Cannabinoid receptor(Intracellular 4th loop region CB1 401-417)
Mutation: C16S / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The source is naturally found in Homo sapiens (human).
References: UniProt: P21554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 5 mM sample in H2O (9:1 H2O/2H2O, pH 3.0). / Solvent system: 70 mM SDS
Sample conditionsIonic strength: no salts used / pH: 3.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert,P.,Mumenthaler, C., Wuthrich, Kstructure solution
XwinNMR3.1BRUKERprocessing
DYANA1.5Guntert,P.,Mumenthaler, C., Wuthrich, Krefinement
RefinementMethod: distance geometry, simulated annealing(DYANA) / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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