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- PDB-2ki9: Human cannabinoid receptor-2 helix 6 -

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Basic information

Entry
Database: PDB / ID: 2ki9
TitleHuman cannabinoid receptor-2 helix 6
ComponentsCannabinoid receptor 2
KeywordsMEMBRANE PROTEIN / Human cannabinoid receptor-2 / GPCR / G-protein coupled receptor
Function / homology
Function and homology information


cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / Class A/1 (Rhodopsin-like receptors) / regulation of metabolic process / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / extrinsic component of cytoplasmic side of plasma membrane / response to amphetamine ...cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / Class A/1 (Rhodopsin-like receptors) / regulation of metabolic process / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / extrinsic component of cytoplasmic side of plasma membrane / response to amphetamine / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / perikaryon / response to lipopolysaccharide / inflammatory response / immune response / dendrite / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Cannabinoid receptor type 2 / 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 2
Similarity search - Component
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDeshmukh, L. / Vinogradova, O. / Tiburu, E.K. / Tyukhtenko, S. / Janero, D.R. / Makriyannis, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural biology of human cannabinoid receptor-2 helix 6 in membrane-mimetic environments.
Authors: Tiburu, E.K. / Tyukhtenko, S. / Deshmukh, L. / Vinogradova, O. / Janero, D.R. / Makriyannis, A.
History
DepositionApr 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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 2


Theoretical massNumber of molelcules
Total (without water)3,5531
Polymers3,5531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 90structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Cannabinoid receptor 2


Mass: 3553.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P34972

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM peptide, 30% TFE, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMpeptide1
30 %TFE1
Sample conditionsPressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, A.T. et al.refinement
X-PLOR NIH2.2Schwieters, C.D. et al.structure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å

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