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P78423

- X3CL1_HUMAN

UniProt

P78423 - X3CL1_HUMAN

Protein

Fractalkine

Gene

CX3CL1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 140 (01 Oct 2014)
      Sequence version 1 (01 May 1997)
      Previous versions | rss
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    Functioni

    The soluble form is chemotactic for T-cells and monocytes, but not for neutrophils. The membrane-bound form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion and migration processes at the endothelium. Binds to CX3CR1.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei339 – 3402Cleavage; to produce soluble formSequence Analysis

    GO - Molecular functioni

    1. chemokine activity Source: UniProtKB
    2. protein binding Source: UniProtKB
    3. receptor binding Source: UniProtKB

    GO - Biological processi

    1. angiogenesis involved in wound healing Source: Ensembl
    2. cell adhesion Source: UniProtKB-KW
    3. chemotaxis Source: UniProtKB
    4. cytokine-mediated signaling pathway Source: UniProtKB
    5. defense response Source: UniProtKB
    6. immune response Source: UniProtKB
    7. leukocyte adhesive activation Source: UniProtKB
    8. leukocyte chemotaxis Source: UniProtKB
    9. lymphocyte chemotaxis Source: Ensembl
    10. macrophage chemotaxis Source: Ensembl
    11. negative regulation of extrinsic apoptotic signaling pathway in absence of ligand Source: Ensembl
    12. neutrophil chemotaxis Source: Ensembl
    13. positive regulation of angiogenesis Source: Ensembl
    14. positive regulation of calcium-independent cell-cell adhesion Source: UniProtKB
    15. positive regulation of inflammatory response Source: UniProtKB
    16. positive regulation of transforming growth factor beta1 production Source: Ensembl

    Keywords - Molecular functioni

    Cytokine

    Keywords - Biological processi

    Cell adhesion, Chemotaxis

    Enzyme and pathway databases

    ReactomeiREACT_15344. Chemokine receptors bind chemokines.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Fractalkine
    Alternative name(s):
    C-X3-C motif chemokine 1
    CX3C membrane-anchored chemokine
    Neurotactin
    Small-inducible cytokine D1
    Cleaved into the following chain:
    Gene namesi
    Name:CX3CL1
    Synonyms:FKN, NTT, SCYD1
    ORF Names:A-152E5.2
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 16

    Organism-specific databases

    HGNCiHGNC:10647. CX3CL1.

    Subcellular locationi

    GO - Cellular componenti

    1. cell surface Source: UniProtKB
    2. extracellular region Source: UniProtKB
    3. extracellular space Source: UniProtKB-KW
    4. integral component of membrane Source: UniProtKB
    5. plasma membrane Source: Reactome

    Keywords - Cellular componenti

    Cell membrane, Membrane, Secreted

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35577.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2424Add
    BLAST
    Chaini25 – 397373FractalkinePRO_0000005252Add
    BLAST
    Chaini25 – ?339315Processed fractalkinePRO_0000296224Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi32 ↔ 581 Publication
    Glycosylationi33 – 331N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi36 ↔ 741 Publication
    Glycosylationi183 – 1831O-linked (GalNAc...)1 Publication
    Glycosylationi253 – 2531O-linked (GalNAc...)2 Publications
    Glycosylationi329 – 3291O-linked (GalNAc...)2 Publications

    Post-translational modificationi

    A soluble short 95 kDa form may be released by proteolytic cleavage from the long membrane-anchored form.By similarity
    O-glycosylated with core 1 or possibly core 8 glycans.2 Publications

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    PaxDbiP78423.
    PeptideAtlasiP78423.
    PRIDEiP78423.

    PTM databases

    PhosphoSiteiP78423.

    Miscellaneous databases

    PMAP-CutDBP78423.

    Expressioni

    Tissue specificityi

    Small intestine, colon, testis, prostate, heart, brain, lung, skeletal muscle, kidney and pancreas.

    Inductioni

    By TNF and IL1/interleukin-1 in pulmonary endothelial cells and umbilical vein endothelial cells.

    Gene expression databases

    ArrayExpressiP78423.
    BgeeiP78423.
    CleanExiHS_CX3CL1.
    GenevestigatoriP78423.

    Organism-specific databases

    HPAiCAB026192.
    HPA040361.

    Interactioni

    Subunit structurei

    Monomer. Interacts with pox virus crmD; this inhibits cell migration mediated by CX3CL1.2 Publications

    Protein-protein interaction databases

    BioGridi112278. 2 interactions.
    DIPiDIP-5878N.
    STRINGi9606.ENSP00000006053.

    Structurei

    Secondary structure

    1
    397
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi34 – 363
    Helixi45 – 473
    Beta strandi48 – 536
    Helixi56 – 583
    Beta strandi59 – 613
    Beta strandi63 – 675
    Turni68 – 703
    Beta strandi72 – 754
    Helixi80 – 9011
    Turni94 – 963

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B2TNMR-A25-100[»]
    1F2LX-ray2.00A/B/C/D25-98[»]
    3ONAX-ray2.60B24-100[»]
    ProteinModelPortaliP78423.
    SMRiP78423. Positions 29-98.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP78423.

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini25 – 341317ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini363 – 39735CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei342 – 36221HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni25 – 10076ChemokineAdd
    BLAST
    Regioni101 – 341241Mucin-like stalkAdd
    BLAST

    Sequence similaritiesi

    Belongs to the intercrine delta family.Curated

    Keywords - Domaini

    Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG46337.
    HOGENOMiHOG000036946.
    HOVERGENiHBG057269.
    InParanoidiP78423.
    KOiK05508.
    OrthoDBiEOG75TMD4.
    PhylomeDBiP78423.
    TreeFamiTF337534.

    Family and domain databases

    InterProiIPR008097. Chemokine_CX3CL1.
    IPR001811. Chemokine_IL8-like_dom.
    [Graphical view]
    PfamiPF00048. IL8. 1 hit.
    [Graphical view]
    PRINTSiPR01721. FRACTALKINE.
    SMARTiSM00199. SCY. 1 hit.
    [Graphical view]
    SUPFAMiSSF54117. SSF54117. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P78423-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAPISLSWLL RLATFCHLTV LLAGQHHGVT KCNITCSKMT SKIPVALLIH    50
    YQQNQASCGK RAIILETRQH RLFCADPKEQ WVKDAMQHLD RQAAALTRNG 100
    GTFEKQIGEV KPRTTPAAGG MDESVVLEPE ATGESSSLEP TPSSQEAQRA 150
    LGTSPELPTG VTGSSGTRLP PTPKAQDGGP VGTELFRVPP VSTAATWQSS 200
    APHQPGPSLW AEAKTSEAPS TQDPSTQAST ASSPAPEENA PSEGQRVWGQ 250
    GQSPRPENSL EREEMGPVPA HTDAFQDWGP GSMAHVSVVP VSSEGTPSRE 300
    PVASGSWTPK AEEPIHATMD PQRLGVLITP VPDAQAATRR QAVGLLAFLG 350
    LLFCLGVAMF TYQSLQGCPR KMAGEMAEGL RYIPRSCGSN SYVLVPV 397
    Length:397
    Mass (Da):42,203
    Last modified:May 1, 1997 - v1
    Checksum:iBAC71F5080DF9CA6
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti240 – 2401A → V.
    Corresponds to variant rs35860084 [ dbSNP | Ensembl ].
    VAR_048714

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U91835 mRNA. Translation: AAB50014.1.
    U84487 mRNA. Translation: AAB49679.1.
    AC004382 Genomic DNA. Translation: AAC24307.1.
    BC001163 mRNA. Translation: AAH01163.1.
    BC016164 mRNA. Translation: AAH16164.1.
    CCDSiCCDS10779.1.
    RefSeqiNP_002987.1. NM_002996.3.
    UniGeneiHs.531668.

    Genome annotation databases

    EnsembliENST00000006053; ENSP00000006053; ENSG00000006210.
    GeneIDi6376.
    KEGGihsa:6376.
    UCSCiuc002eli.3. human.

    Polymorphism databases

    DMDMi6175080.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    Wikipedia

    CX3CL1 entry

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U91835 mRNA. Translation: AAB50014.1 .
    U84487 mRNA. Translation: AAB49679.1 .
    AC004382 Genomic DNA. Translation: AAC24307.1 .
    BC001163 mRNA. Translation: AAH01163.1 .
    BC016164 mRNA. Translation: AAH16164.1 .
    CCDSi CCDS10779.1.
    RefSeqi NP_002987.1. NM_002996.3.
    UniGenei Hs.531668.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B2T NMR - A 25-100 [» ]
    1F2L X-ray 2.00 A/B/C/D 25-98 [» ]
    3ONA X-ray 2.60 B 24-100 [» ]
    ProteinModelPortali P78423.
    SMRi P78423. Positions 29-98.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 112278. 2 interactions.
    DIPi DIP-5878N.
    STRINGi 9606.ENSP00000006053.

    PTM databases

    PhosphoSitei P78423.

    Polymorphism databases

    DMDMi 6175080.

    Proteomic databases

    PaxDbi P78423.
    PeptideAtlasi P78423.
    PRIDEi P78423.

    Protocols and materials databases

    DNASUi 6376.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000006053 ; ENSP00000006053 ; ENSG00000006210 .
    GeneIDi 6376.
    KEGGi hsa:6376.
    UCSCi uc002eli.3. human.

    Organism-specific databases

    CTDi 6376.
    GeneCardsi GC16P057406.
    HGNCi HGNC:10647. CX3CL1.
    HPAi CAB026192.
    HPA040361.
    MIMi 601880. gene.
    neXtProti NX_P78423.
    PharmGKBi PA35577.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG46337.
    HOGENOMi HOG000036946.
    HOVERGENi HBG057269.
    InParanoidi P78423.
    KOi K05508.
    OrthoDBi EOG75TMD4.
    PhylomeDBi P78423.
    TreeFami TF337534.

    Enzyme and pathway databases

    Reactomei REACT_15344. Chemokine receptors bind chemokines.

    Miscellaneous databases

    EvolutionaryTracei P78423.
    GeneWikii CX3CL1.
    GenomeRNAii 6376.
    NextBioi 24772.
    PMAP-CutDB P78423.
    PROi P78423.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P78423.
    Bgeei P78423.
    CleanExi HS_CX3CL1.
    Genevestigatori P78423.

    Family and domain databases

    InterProi IPR008097. Chemokine_CX3CL1.
    IPR001811. Chemokine_IL8-like_dom.
    [Graphical view ]
    Pfami PF00048. IL8. 1 hit.
    [Graphical view ]
    PRINTSi PR01721. FRACTALKINE.
    SMARTi SM00199. SCY. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54117. SSF54117. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    4. "Enrichment of glycopeptides for glycan structure and attachment site identification."
      Nilsson J., Rueetschi U., Halim A., Hesse C., Carlsohn E., Brinkmalm G., Larson G.
      Nat. Methods 6:809-811(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT SER-253 AND THR-329, STRUCTURE OF CARBOHYDRATES.
      Tissue: Cerebrospinal fluid.
    5. "Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD."
      Halim A., Nilsson J., Ruetschi U., Hesse C., Larson G.
      Mol. Cell. Proteomics 0:0-0(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCOSYLATION AT THR-183; SER-253 AND THR-329, STRUCTURE OF CARBOHYDRATES, IDENTIFICATION BY MASS SPECTROMETRY.
    6. "Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1."
      Mizoue L.S., Bazan J.F., Johnson E.C., Handel T.M.
      Biochemistry 38:1402-1414(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 25-100, SUBUNIT, INTERACTION WITH CX3CR1.
    7. "The crystal structure of the chemokine domain of fractalkine shows a novel quaternary arrangement."
      Hoover D.M., Mizoue L.S., Handel T.M., Lubkowski J.
      J. Biol. Chem. 275:23187-23193(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-98, DISULFIDE BONDS.
    8. "Structural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor."
      Xue X., Lu Q., Wei H., Wang D., Chen D., He G., Huang L., Wang H., Wang X.
      PLoS Pathog. 7:E1002162-E1002162(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 24-100 IN COMPLEX WITH POX VIRUS CRMD, FUNCTION, INTERACTION WITH VIRAL CRMD.

    Entry informationi

    Entry nameiX3CL1_HUMAN
    AccessioniPrimary (citable) accession number: P78423
    Secondary accession number(s): O00672
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: May 1, 1997
    Last modified: October 1, 2014
    This is version 140 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 16
      Human chromosome 16: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3