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P78423

- X3CL1_HUMAN

UniProt

P78423 - X3CL1_HUMAN

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Protein

Fractalkine

Gene
CX3CL1, FKN, NTT, SCYD1, A-152E5.2
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 form Reviewed prediction

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
Complete GO annotation...

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 341317Extracellular Reviewed predictionAdd
BLAST
Transmembranei342 – 36221Helical; Reviewed predictionAdd
BLAST
Topological domaini363 – 39735Cytoplasmic Reviewed predictionAdd
BLAST

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
Complete GO annotation...

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...) Reviewed prediction
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.1 Publication

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.

Miscellaneous databases

EvolutionaryTraceiP78423.

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.

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 139 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

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