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(-) Description

Title :  SOLUTION STRUCTURE OF THE CHEMOKINE CCL21
 
Authors :  C. T. Veldkamp, F. C. Peterson, M. Love, J. L. Sandberg
Date :  10 Oct 10  (Deposition) - 02 Nov 11  (Release) - 16 Sep 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Slc, 6Ckine, Exodus-2, Ccr7, Chemokine, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Love, J. L. Sandberg, J. J. Ziarek, K. P. Gerarden, R. R. Rode, D. R. Jensen, D. R. Mccaslin, F. C. Peterson, C. T. Veldkamp
Solution Structure Of Ccl21 And Identification Of A Putativ Ccr7 Binding Site.
Biochemistry V. 51 733 2012
PubMed-ID: 22221265  |  Reference-DOI: 10.1021/BI201601K

(-) Compounds

Molecule 1 - C-C MOTIF CHEMOKINE 21
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPQE30-8HT-SMT3
    Expression System Vector TypePLASMID
    FragmentCCL21 (UNP RESIDUES 24-134)
    GeneCCL21, RP11-195F19.22-001, SCYA21, UNQ784/PRO1600
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym6CKINE, BETA-CHEMOKINE EXODUS-2, SECONDARY LYMPHOID-TISSUE CHEMOKINE, SLC, SMALL-INDUCIBLE CYTOKINE A21

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L4N)

(-) Sites  (0, 0)

(no "Site" information available for 2L4N)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:8 -A:34
2A:9 -A:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L4N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2L4N)

(-) Exons   (0, 0)

(no "Exon" information available for 2L4N)

(-) 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:70
 aligned with CCL21_HUMAN | O00585 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:70
                                    33        43        53        63        73        83        93
           CCL21_HUMAN   24 SDGGAQDCCLKYSQRKIPAKVVRSYRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWVQQLMQHLDKT 93
               SCOP domains d2l4na_ A: automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee...........eeeee.......eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  2l4n A  1 SDGGAQDCCLKYSQRKIPAKVVRSYRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWVQQLMQHLDKT 70
                                    10        20        30        40        50        60        70

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 2L4N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L4N)

(-) Gene Ontology  (53, 53)

NMR Structure(hide GO term definitions)
Chain A   (CCL21_HUMAN | O00585)
molecular function
    GO:0048020    CCR chemokine receptor binding    Interacting selectively and non-covalently with a CCR chemokine receptor.
    GO:0031732    CCR7 chemokine receptor binding    Interacting selectively and non-covalently with a CCR7 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:0042379    chemokine receptor binding    Interacting selectively and non-covalently with any chemokine receptor.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
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:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0060326    cell chemotaxis    The directed movement of a motile 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:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    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:0002407    dendritic cell chemotaxis    The movement of a dendritic cell in response to an external stimulus.
    GO:0097026    dendritic cell dendrite assembly    Formation of dendrites, branched cellular projections (or cytoplasmic extension) that are extended from the surface of a dendritic immune cell, and which enable the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells.
    GO:0001768    establishment of T cell polarity    The directed orientation of T cell signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with antigen presenting cell.
    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:0001771    immunological synapse formation    The formation of an area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and target cell, which facilitates activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    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:0035759    mesangial cell-matrix adhesion    The binding of a mesangial cell to the extracellular matrix via adhesion molecules. A mesangial cell is a cell that encapsulates the capillaries and venules in the kidney.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:2000548    negative regulation of dendritic cell dendrite assembly    Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell dendrite assembly.
    GO:2000107    negative regulation of leukocyte apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process.
    GO:1903237    negative regulation of leukocyte tethering or rolling    Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte tethering or rolling.
    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:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0033630    positive regulation of cell adhesion mediated by integrin    Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:2000147    positive regulation of cell motility    Any process that activates or increases the frequency, rate or extent of cell motility.
    GO:0001954    positive regulation of cell-matrix adhesion    Any process that activates or increases the rate or extent of cell adhesion to an extracellular matrix.
    GO:0050921    positive regulation of chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
    GO:0002606    positive regulation of dendritic cell antigen processing and presentation    Any process that activates or increases the frequency, rate, or extent of dendritic cell antigen processing and presentation.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0010560    positive regulation of glycoprotein biosynthetic process    Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
    GO:2000529    positive regulation of myeloid dendritic cell chemotaxis    Any process that activates or increases the frequency, rate or extent of myeloid dendritic cell chemotaxis.
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is 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:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0031274    positive regulation of pseudopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0051209    release of sequestered calcium ion into cytosol    The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.
    GO:0034695    response to prostaglandin E    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 a prostagladin E stimulus.
    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.
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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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        CCL21_HUMAN | O005855eki

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