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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURES OF THYMUS AND ACTIVATION-REGULATED CHEMOKINE
 
Authors :  O. A. Asojo, C. Boulegue, D. M. Hoover, W. Lu, J. Lubkowski
Date :  23 Jan 03  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tarc, Chemokine, Cytokine, Cc-Chemokine, Chemotaxis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. A. Asojo, C. Boulegue, D. M. Hoover, W. Lu, J. Lubkowski
Structures Of Thymus And Activation-Regulated Chemokine (Tarc).
Acta Crystallogr. , Sect. D V. 59 1165 2003
PubMed-ID: 12832759  |  Reference-DOI: 10.1107/S0907444903009454
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMUS AND ACTIVATION-REGULATED CHEMOKINE
    ChainsA, B
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS
    SynonymSMALL INDUCIBLE CYTOKINE A17
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NR2)

(-) Sites  (0, 0)

(no "Site" information available for 1NR2)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:10 -A:34
2A:11 -A:50
3B:10 -B:34
4B:11 -B:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NR2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048709V67MCCL17_HUMANPolymorphism34379253A/BV44M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048709V67MCCL17_HUMANPolymorphism34379253AV44M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048709V67MCCL17_HUMANPolymorphism34379253BV44M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL17_HUMAN33-74
 
  2A:10-51
B:10-51
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL17_HUMAN33-74
 
  1A:10-51
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL17_HUMAN33-74
 
  1-
B:10-51

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002192441ENSE00001518386chr16:57438679-5743874870CCL17_HUMAN-00--
1.2bENST000002192442bENSE00001298183chr16:57447786-57447914129CCL17_HUMAN1-24240--
1.3ENST000002192443ENSE00000685201chr16:57448993-57449110118CCL17_HUMAN24-63402A:8-40
B:8-40
33
33
1.4ENST000002192444ENSE00001290890chr16:57449677-57449974298CCL17_HUMAN63-94322A:40-69
B:40-69
30
30

(-) Sequences/Alignments

Asymmetric Unit
   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:62
 aligned with CCL17_HUMAN | Q92583 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:62
                                    40        50        60        70        80        90  
           CCL17_HUMAN   31 RECCLEYFKGAIPLRKLKTWYQTSEDCSRDAIVFVTVQGRAICSDPNNKRVKNAVKYLQSLE 92
               SCOP domains d1nr2a_ A: Thymus and activation-regulated chemokine, TRAC     SCOP domains
               CATH domains 1nr2A00 A:8-69  [code=2.40.50.40, no name defined]             CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee.........eeeee....eeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------M------------------------- SAPs(SNPs)
                    PROSITE --SMALL_CYTOKINES_CC  PDB: A:10-51          ------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:8-40            ----------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.4  PDB: A:40-69         Transcript 1 (2)
                  1nr2 A  8 RECCLEYFKGAIPLRKLKTWYQTSEDCSRDAIVFVTVQGRAICSDPNNKRVKNAVKYLQSLE 69
                                    17        27        37        47        57        67  

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with CCL17_HUMAN | Q92583 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:62
                                    40        50        60        70        80        90  
           CCL17_HUMAN   31 RECCLEYFKGAIPLRKLKTWYQTSEDCSRDAIVFVTVQGRAICSDPNNKRVKNAVKYLQSLE 92
               SCOP domains d1nr2b_ B: Thymus and activation-regulated chemokine, TRAC     SCOP domains
               CATH domains 1nr2B00 B:8-69  [code=2.40.50.40, no name defined]             CATH domains
           Pfam domains (1) IL8-1nr2B01 B:8-65                                        ---- Pfam domains (1)
           Pfam domains (2) IL8-1nr2B02 B:8-65                                        ---- Pfam domains (2)
         Sec.struct. author ................eeeeee.........eeeee....eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------M------------------------- SAPs(SNPs)
                    PROSITE --SMALL_CYTOKINES_CC  PDB: B:10-51          ------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:8-40            ----------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.4  PDB: B:40-69         Transcript 1 (2)
                  1nr2 B  8 RECCLEYFKGAIPLRKLKTWYQTSEDCSRDAIVFVTVQGRAICSDPNNKRVKNAVKYLQSLE 69
                                    17        27        37        47        57        67  

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CCL17_HUMAN | Q92583)
molecular function
    GO:0048020    CCR chemokine receptor binding    Interacting selectively and non-covalently with a CCR chemokine receptor.
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0071346    cellular response to interferon-gamma    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
    GO:0071347    cellular response to interleukin-1    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0048247    lymphocyte chemotaxis    The directed movement of a lymphocyte in response to an external stimulus.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045662    negative regulation of myoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCL17_HUMAN | Q925831nr4

(-) Related Entries Specified in the PDB File

1nr4 TARC STRUCTURE IN P 1