Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  HUMAN CANNABINOID RECEPTOR-2 HELIX 6
 
Authors :  L. Deshmukh, O. Vinogradova, E. K. Tiburu, S. Tyukhtenko, D. R. Janero, A. Makriyannis
Date :  28 Apr 09  (Deposition) - 12 May 09  (Release) - 02 Jun 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Human Cannabinoid Receptor-2, Gpcr, G-Protein Coupled Receptor, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. K. Tiburu, S. Tyukhtenko, L. Deshmukh, O. Vinogradova, D. R. Janero, A. Makriyannis
Structural Biology Of Human Cannabinoid Receptor-2 Helix 6 In Membrane-Mimetic Environments.
Biochem. Biophys. Res. Commun. V. 384 243 2009
PubMed-ID: 19397896  |  Reference-DOI: 10.1016/J.BBRC.2009.04.099
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CANNABINOID RECEPTOR 2
    ChainsA
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KI9)

(-) Sites  (0, 0)

(no "Site" information available for 2KI9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KI9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KI9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KI9)

(-) Exons   (0, 0)

(no "Exon" information available for 2KI9)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:33
 aligned with CNR2_HUMAN | P34972 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:33
                                   249       259       269   
           CNR2_HUMAN   240 DVRLAKTLGLVLAVLLICWFPVLALMAHSLATT 272
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains 7tm_1-2ki9A01 A:1-33              Pfam domains
         Sec.struct. author .....hhhhhhhhhhh....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 2ki9 A   1 DVRLAKTLGLVLAVLLICWFPVLALMAHSLATT  33
                                    10        20        30   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2KI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KI9)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: GPCR_A (90)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (CNR2_HUMAN | P34972)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0004949    cannabinoid receptor activity    Combining with a cannabinoid to initiate a change in cell activity. Cannabinoids are a class of diverse chemical compounds that include the endocannabinoids and the phytocannabinoids.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007187    G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation or inhibition of a nucleotide cyclase activity and a subsequent change in the concentration of a cyclic nucleotide.
    GO:0038171    cannabinoid signaling pathway    The series of molecular signals generated as a consequence of a cannabinoid binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription. Cannabinoids are a class of diverse chemical compounds that include the endocannabinoids and the phytocannabinoids.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045759    negative regulation of action potential    Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0033004    negative regulation of mast cell activation    Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell activation.
    GO:0051001    negative regulation of nitric-oxide synthase activity    Any process that stops or reduces the activity of the enzyme nitric-oxide synthase.
    GO:0032229    negative regulation of synaptic transmission, GABAergic    Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    GO:0001975    response to amphetamine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2ki9)
 
  Sites
(no "Sites" information available for 2ki9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ki9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ki9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CNR2_HUMAN | P34972
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CNR2_HUMAN | P34972
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2KI9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KI9)