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(-) Description

Title :  CRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE
 
Authors :  D. M. Hoover, L. S. Mizoue, T. M. Handel, J. Lubkowski
Date :  26 May 00  (Deposition) - 06 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Chemoattractant, X-Ray Structure, Fractalkine, Neurotactin, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Hoover, L. S. Mizoue, T. M. Handel, J. Lubkowski
The Crystal Structure Of The Chemokine Domain Of Fractalkine Shows A Novel Quaternary Arrangement.
J. Biol. Chem. V. 275 23187 2000
PubMed-ID: 10770945  |  Reference-DOI: 10.1074/JBC.M002584200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRACTALKINE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAED4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHEMOKINE DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEUROTACTIN, CX3C MEMBRANE-ANCHORED CHEMOKINE, SMALL INDUCIBLE CYTOKINE D1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F2L)

(-) Sites  (0, 0)

(no "Site" information available for 1F2L)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:34
2A:12 -A:50
3B:8 -B:34
4B:12 -B:50
5C:8 -C:34
6C:12 -C:50
7D:8 -D:34
8D:12 -D:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F2L)

(-) Exons   (2, 8)

Asymmetric/Biological Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000000060531ENSE00001301983chr16:57406375-57406550176X3CL1_HUMAN1-24240--
1.2ENST000000060532ENSE00000685198chr16:57413546-57413666121X3CL1_HUMAN24-64414A:5-40
B:5-40
C:5-40
D:5-40		36
36
36
36
1.3ENST000000060533ENSE00001317056chr16:57415942-574189603019X3CL1_HUMAN64-3973344A:40-68
B:40-68
C:40-68
D:40-74		29
29
29
35

(-) Sequences/Alignments

Asymmetric/Biological 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:64
 aligned with X3CL1_HUMAN | P78423 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:64
                                    38        48        58        68        78        88    
           X3CL1_HUMAN   29 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 92
               SCOP domains d1f2la_ A: Chemokine domain of fractalkine                       SCOP domains
               CATH domains 1f2lA00 A:5-68  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhh.eeeeee.hhhhh...eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:5-40 UniProt: 24-64---------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: A:40-68        Transcript 1 (2)
                  1f2l A  5 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 68
                                    14        24        34        44        54        64    


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with X3CL1_HUMAN | P78423 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:64
                                    38        48        58        68        78        88    
           X3CL1_HUMAN   29 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 92
               SCOP domains d1f2lb_ B: Chemokine domain of fractalkine                       SCOP domains
               CATH domains 1f2lB00 B:5-68  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.......hhh.eeeeee.hhhhh...eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:5-40 UniProt: 24-64---------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: B:40-68        Transcript 1 (2)
                  1f2l B  5 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 68
                                    14        24        34        44        54        64    


Chain C from PDB  Type:PROTEIN  Length:64
 aligned with X3CL1_HUMAN | P78423 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:64
                                    38        48        58        68        78        88    
           X3CL1_HUMAN   29 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 92
               SCOP domains d1f2lc_ C: Chemokine domain of fractalkine                       SCOP domains
               CATH domains 1f2lC00 C:5-68  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee........hhh.eeeeee.hhhhh...eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:5-40 UniProt: 24-64---------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: C:40-68        Transcript 1 (2)
                  1f2l C  5 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ 68
                                    14        24        34        44        54        64    


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with X3CL1_HUMAN | P78423 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:70
                                    38        48        58        68        78        88        98
           X3CL1_HUMAN   29 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTR 98
               SCOP domains d1f2ld_ D: Chemokine domain of fractalkine                             SCOP domains
               CATH domains 1f2lD00 D:5-74  [code=2.40.50.40, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhh.eeeeee.hhhhh...eeeee....eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:5-40 UniProt: 24-64---------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: D:40-74 [INCOMPLETE] Transcript 1 (2)
                  1f2l D  5 VTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTR 74
                                    14        24        34        44        54        64        74
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F2L)

(-) Gene Ontology  (57, 57)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (X3CL1_HUMAN | P78423)
molecular function
    GO:0048020    CCR chemokine receptor binding    Interacting selectively and non-covalently with a CCR chemokine receptor.
    GO:0031737    CX3C chemokine receptor binding    Interacting selectively and non-covalently with a CX3C 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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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: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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0060055    angiogenesis involved in wound healing    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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: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:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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:0060080    inhibitory postsynaptic potential    A process that causes a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential.
    GO:0033622    integrin activation    The aggregation, arrangement and bonding together of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, that lead to the increased affinity of the integrin for its extracellular ligands.
    GO:0050902    leukocyte adhesive activation    The activation of loosely bound or rolling leukocytes by signals displayed on blood vessel endothelial cells, which is typically the second step in cellular extravasation.
    GO:0030595    leukocyte chemotaxis    The movement of a leukocyte in response to an external stimulus.
    GO:0002523    leukocyte migration involved in inflammatory response    The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
    GO:0048247    lymphocyte chemotaxis    The directed movement of a lymphocyte in response to an external stimulus.
    GO:0048246    macrophage chemotaxis    The movement of a macrophage in response to an external stimulus.
    GO:0001774    microglial cell activation    The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0050710    negative regulation of cytokine secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0045906    negative regulation of vasoconstriction    Any process that stops, prevents, or reduces the frequency, rate or extent of vasoconstriction.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    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.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0051041    positive regulation of calcium-independent cell-cell adhesion    Any process that activates or increases the frequency, rate or extent of calcium-independent cell-cell adhesion.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0010759    positive regulation of macrophage chemotaxis    Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
    GO:0002052    positive regulation of neuroblast proliferation    Any process that activates or increases the rate of neuroblast proliferation.
    GO:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    GO:0032914    positive regulation of transforming growth factor beta1 production    Any process that activates or increases the frequency, rate, or extent of production of transforming growth factor-beta1.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, 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.
    GO:0098794    postsynapse    The part of a synapse that is part of the post-synaptic cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        X3CL1_HUMAN | P78423: 1b2t 3ona 4xt1 4xt3

(-) Related Entries Specified in the PDB File

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