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(-) Description

Title :  NMR STRUCTURE OF CXC CHEMOKINE CXCL11/ITAC
 
Authors :  V. Booth, I. Clark-Lewis, B. D. Sykes
Date :  20 Nov 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Chemokine, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Booth, I. Clark-Lewis, B. D. Sykes
Nmr Structure Of Cxcr3 Binding Chemokine Cxcl11 (Itac).
Protein Sci. V. 13 2022 2004
PubMed-ID: 15273303  |  Reference-DOI: 10.1110/PS.04791404
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMALL INDUCIBLE CYTOKINE B11
    ChainsA
    EngineeredYES
    Other DetailsSYNTHESIZED WITH N15 ISOTOPE LABELS ON ALL LEUCINE AND VALINE RESIDUES. SEQUENCE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymCXCL11, INTERFERON-INDUCIBLE T-CELL ALPHA CHEMOATTRACTANT, I-TAC, INTERFERON-GAMMA-INDUCIBLE PROTEIN- 9, IP-9, H174, BETA-R1
    SyntheticYES

 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 1RJT)

(-) Sites  (0, 0)

(no "Site" information available for 1RJT)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:9 -A:36
2A:11 -A:53

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048700N55SCXL11_HUMANPolymorphism4859596AN34S

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.CXL11_HUMAN30-76  1A:9-55

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003066212aENSE00001126440chr4:76957350-76957080271CXL11_HUMAN1-21210--
1.3ENST000003066213ENSE00001139467chr4:76956495-76956369127CXL11_HUMAN21-63431A:1-4242
1.4ENST000003066214ENSE00001126433chr4:76956272-7695620073CXL11_HUMAN63-87251A:42-6625
1.5cENST000003066215cENSE00001139458chr4:76955969-769548351135CXL11_HUMAN88-9471A:67-737

(-) 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:73
 aligned with CXL11_HUMAN | O14625 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:73
                                    31        41        51        61        71        81        91   
           CXL11_HUMAN   22 FPMFKRGRCLCIGPGVKAVKVADIEKASIMYPSNNCDKIEVIITLKENKGQRCLNPKSKQARLIIKKVERKNF 94
               SCOP domains d1rjta_ A: Small inducible cytokine b11 (CXCL11/I-TAC)                    SCOP domains
               CATH domains 1rjtA00 A:1-73  [code=2.40.50.40, no name defined]                        CATH domains
               Pfam domains --IL8-1rjtA01 A:3-68                                                ----- Pfam domains
         Sec.struct. author ...........................................................hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------S--------------------------------------- SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CXC  PDB: A:9-55 UniProt: 30-76------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-42 UniProt: 21-63      ------------------------1.5c    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.4  PDB: A:42-66   ------- Transcript 1 (2)
                  1rjt A  1 FPMFKRGRCLCIGPGVKAVKVADIEKASIMYPSNNCDKIEVIITLKENKGQRCLNPKSKQARLIIKKVERKNF 73
                                    10        20        30        40        50        60        70   

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (CXL11_HUMAN | O14625)
molecular function
    GO:0048248    CXCR3 chemokine receptor binding    Interacting selectively and non-covalently with a the CXCR3 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:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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).
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:0010818    T cell chemotaxis    The directed movement of a T cell in response to an external stimulus. A T cell is a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
    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: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:0030816    positive regulation of cAMP metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0043950    positive regulation of cAMP-mediated signaling    Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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: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: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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