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(-) Description

Title :  S1P4 FIRST EXTRACELLULAR LOOP PEPTIDOMIMETIC
 
Authors :  T. C. T. Pham, R. W. Kriwacki, A. L. Parrill
Date :  11 Jan 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Coiled Coil, Disulfide, Helix-Turn-Helix, 3-10 Helix, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. C. T. Pham, R. W. Kriwacki, A. L. Parrill
Peptide Design And Structural Characterization Of A Gpcr Loop Mimetic
Biopolymers V. 86 298 2007
PubMed-ID: 17443712  |  Reference-DOI: 10.1002/BIP.20745
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S1P4 FIRST EXTRACELLULAR LOOP PEPTIDOMIMETIC
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-32A, CCE1A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR LOOP 1
    GeneS1P4
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS PROTEIN IS A FUSION PROTEIN. RESIDUES 13-26 AND 29-30 ARE FROM THE FIRST EXTRACELLULAR LOOP OF S1P4 RECEPTOR. THE REST, RESIDUES 3-12, 27-28, AND 31-34 ARE FROM ARFATIN (PDB ENTRY 1I49) SEGMENTS 139-148, 164- 164, 168-171 OF 1I49 THAT WE DESIGNED TO BE IN THE SEQUENCE.
    SynonymARFAPTIN-2, ADP-RIBOSYLATION FACTOR-INTERACTING PROTEIN 2, PARTNER OF RAC1, PROTEIN POR1PHINGOSINE 1- PHOSPHATE RECEPTOR EDG-6, S1P RECEPTOR EDG-6, ENDOTHELIAL DIFFERENTIATION G-PROTEIN COUPLED RECEPTOR 6, SPHINGOSINE 1-PHOSPHATE RECEPTOR 4, S1P4

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DCO)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:10 -A:28

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002461151ENSE00000859542chr19:3178766-31803291564S1PR4_HUMAN1-3933931A:1-34 (gaps)85

(-) 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:34
 aligned with ARFP2_HUMAN | P53365 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:74
                                   210       220       230       240       250       260       270    
          ARFP2_HUMAN   201 GAVNFFVSSINTLVTKTMEDTLMTVKQYEAARLEYDAYRTDLEELSLGPRDAGTRGRLESAQATFQAHRDKYEK 274
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------------------hhhhhhhhhhhhh-hhhhh----h......h---hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2dco A   1 G--------------------------------SYDAYRTDCEELS-GARTF----RLAPAQWS---CRETFQA  34
                            |        -         -         -   |     8     | |17 |    | 23   |   |30    
                            |                                2          14 |  19   20     27  28      
                            1                                             15                          

Chain A from PDB  Type:PROTEIN  Length:34
 aligned with S1PR4_HUMAN | O95977 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:85
                                    53        63        73        83        93       103       113       123     
          S1PR4_HUMAN    44 GGLGALRGLSVAASCLVVLENLLVLAAITSHMRSRRWVYYCLVNITLSDLLTGAAYLANVLLSGARTFRLAPAQWFLREGLLFTA 128
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh-----hhh----hhh----------------------------------------hhhhhhh......hhhh--hh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-34 (gaps) UniProt: 1-393 [INCOMPLETE]                              Transcript 1
                 2dco A   1 GSYDAYR-----TDC----EEL----------------------------------------SGARTFRLAPAQWSCRE--TFQA  34
                                  |  -  | |   11 |       -         -         -         -  |     21        |- |   
                                  7     8 |   11 |                                       14              30 31   
                                         10     13                                                               

   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 2DCO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DCO)

(-) Gene Ontology  (32, 33)

NMR Structure(hide GO term definitions)
Chain A   (ARFP2_HUMAN | P53365)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0030742    GTP-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP.
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0034315    regulation of Arp2/3 complex-mediated actin nucleation    Any process that modulates the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.

Chain A   (S1PR4_HUMAN | O95977)
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:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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.
    GO:0038036    sphingosine-1-phosphate receptor activity    Combining with the sphingolipid sphingosine-1-phosphate (S1P), and transmitting the signal across the membrane by activating an associated G-protein.
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:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0007189    adenylate cyclase-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP).
    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:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    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.
    GO:0003376    sphingosine-1-phosphate signaling pathway    A series of molecular signals initiated by the sphingolipid sphingosine-1-phosphate (S1P) binding to a receptor on the surface of the cell, and which proceeds with the activated receptor transmitting the signal by promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARFP2_HUMAN | P533651i49 1i4d 1i4l 1i4t 4dcn

(-) Related Entries Specified in the PDB File

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