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P78423 (X3CL1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 135. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:

  1. Processed fractalkine
Gene names
Name:CX3CL1
Synonyms:FKN, NTT, SCYD1
ORF Names:A-152E5.2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length397 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8

Subunit structure

Monomer. Interacts with pox virus crmD; this inhibits cell migration mediated by CX3CL1. Ref.6 Ref.8

Subcellular location

Cell membrane; Single-pass type I membrane protein.

Processed fractalkine: Secreted.

Tissue specificity

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

Induction

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

Post-translational modification

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. Ref.5

Sequence similarities

Belongs to the intercrine delta family.

Ontologies

Keywords
   Biological processCell adhesion
Chemotaxis
   Cellular componentCell membrane
Membrane
Secreted
   Coding sequence diversityPolymorphism
   DomainSignal
Transmembrane
Transmembrane helix
   Molecular functionCytokine
   PTMDisulfide bond
Glycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processangiogenesis involved in wound healing

Inferred from electronic annotation. Source: Ensembl

cell adhesion

Inferred from electronic annotation. Source: UniProtKB-KW

cytokine-mediated signaling pathway

Traceable author statement PubMed 11777952. Source: UniProtKB

defense response

Traceable author statement PubMed 12714508. Source: UniProtKB

immune response

Traceable author statement PubMed 12714508. Source: UniProtKB

leukocyte adhesive activation

Traceable author statement PubMed 12714508. Source: UniProtKB

leukocyte chemotaxis

Traceable author statement PubMed 11777952. Source: UniProtKB

lymphocyte chemotaxis

Inferred from electronic annotation. Source: Ensembl

macrophage chemotaxis

Inferred from electronic annotation. Source: Ensembl

negative regulation of extrinsic apoptotic signaling pathway in absence of ligand

Inferred from electronic annotation. Source: Ensembl

neutrophil chemotaxis

Inferred from electronic annotation. Source: Ensembl

positive regulation of angiogenesis

Inferred from electronic annotation. Source: Ensembl

positive regulation of calcium-independent cell-cell adhesion

Inferred from direct assay PubMed 12714508. Source: UniProtKB

positive regulation of inflammatory response

Inferred from expression pattern PubMed 11777952. Source: UniProtKB

positive regulation of transforming growth factor beta1 production

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentcell surface

Inferred from direct assay PubMed 12714508. Source: UniProtKB

extracellular region

Inferred from direct assay PubMed 12714508. Source: UniProtKB

extracellular space

Inferred from electronic annotation. Source: UniProtKB-KW

integral component of membrane

Inferred from direct assay PubMed 12714508. Source: UniProtKB

plasma membrane

Traceable author statement. Source: Reactome

   Molecular_functionchemokine activity

Inferred from direct assay Ref.8. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2424
Chain25 – 397373Fractalkine
PRO_0000005252
Chain25 – ?339315Processed fractalkine
PRO_0000296224

Regions

Topological domain25 – 341317Extracellular Potential
Transmembrane342 – 36221Helical; Potential
Topological domain363 – 39735Cytoplasmic Potential
Region25 – 10076Chemokine
Region101 – 341241Mucin-like stalk

Sites

Site339 – 3402Cleavage; to produce soluble form Potential

Amino acid modifications

Glycosylation331N-linked (GlcNAc...) Potential
Glycosylation1831O-linked (GalNAc...) Ref.5
Glycosylation2531O-linked (GalNAc...) Ref.4 Ref.5
Glycosylation3291O-linked (GalNAc...) Ref.4 Ref.5
Disulfide bond32 ↔ 58 Ref.7
Disulfide bond36 ↔ 74 Ref.7

Natural variations

Natural variant2401A → V.
Corresponds to variant rs35860084 [ dbSNP | Ensembl ].
VAR_048714

Secondary structure

.................. 397
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P78423 [UniParc].

Last modified May 1, 1997. Version 1.
Checksum: BAC71F5080DF9CA6

FASTA39742,203
        10         20         30         40         50         60 
MAPISLSWLL RLATFCHLTV LLAGQHHGVT KCNITCSKMT SKIPVALLIH YQQNQASCGK 

        70         80         90        100        110        120 
RAIILETRQH RLFCADPKEQ WVKDAMQHLD RQAAALTRNG GTFEKQIGEV KPRTTPAAGG 

       130        140        150        160        170        180 
MDESVVLEPE ATGESSSLEP TPSSQEAQRA LGTSPELPTG VTGSSGTRLP PTPKAQDGGP 

       190        200        210        220        230        240 
VGTELFRVPP VSTAATWQSS APHQPGPSLW AEAKTSEAPS TQDPSTQAST ASSPAPEENA 

       250        260        270        280        290        300 
PSEGQRVWGQ GQSPRPENSL EREEMGPVPA HTDAFQDWGP GSMAHVSVVP VSSEGTPSRE 

       310        320        330        340        350        360 
PVASGSWTPK AEEPIHATMD PQRLGVLITP VPDAQAATRR QAVGLLAFLG LLFCLGVAMF 

       370        380        390 
TYQSLQGCPR KMAGEMAEGL RYIPRSCGSN SYVLVPV 

« Hide

References

« Hide 'large scale' references
[1]"A new class of membrane-bound chemokine with a CX3C motif."
Bazan J.F., Bacon K.B., Hardiman G., Wang W., Soo K., Rossi D., Greaves D.R., Zlotnik A., Schall T.J.
Nature 385:640-644(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q."
Loftus B.J., Kim U.-J., Sneddon V.P., Kalush F., Brandon R., Fuhrmann J., Mason T., Crosby M.L., Barnstead M., Cronin L., Mays A.D., Cao Y., Xu R.X., Kang H.-L., Mitchell S., Eichler E.E., Harris P.C., Venter J.C., Adams M.D.
Genomics 60:295-308(1999) [PubMed] [Europe PMC] [Abstract]
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, 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.
+Additional computationally mapped references.

Web resources

Wikipedia

CX3CL1 entry

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_002987.1. NM_002996.3.
UniGeneHs.531668.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1B2TNMR-A25-100[»]
1F2LX-ray2.00A/B/C/D25-98[»]
3ONAX-ray2.60B24-100[»]
ProteinModelPortalP78423.
SMRP78423. Positions 29-98.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112278. 2 interactions.
DIPDIP-5878N.
STRING9606.ENSP00000006053.

PTM databases

PhosphoSiteP78423.

Polymorphism databases

DMDM6175080.

Proteomic databases

PaxDbP78423.
PeptideAtlasP78423.
PRIDEP78423.

Protocols and materials databases

DNASU6376.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000006053; ENSP00000006053; ENSG00000006210.
GeneID6376.
KEGGhsa:6376.
UCSCuc002eli.3. human.

Organism-specific databases

CTD6376.
GeneCardsGC16P057406.
HGNCHGNC:10647. CX3CL1.
HPACAB026192.
HPA040361.
MIM601880. gene.
neXtProtNX_P78423.
PharmGKBPA35577.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG46337.
HOGENOMHOG000036946.
HOVERGENHBG057269.
InParanoidP78423.
KOK05508.
OrthoDBEOG75TMD4.
PhylomeDBP78423.
TreeFamTF337534.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.

Gene expression databases

ArrayExpressP78423.
BgeeP78423.
CleanExHS_CX3CL1.
GenevestigatorP78423.

Family and domain databases

InterProIPR008097. Chemokine_CX3CL1.
IPR001811. Chemokine_IL8-like_dom.
[Graphical view]
PfamPF00048. IL8. 1 hit.
[Graphical view]
PRINTSPR01721. FRACTALKINE.
SMARTSM00199. SCY. 1 hit.
[Graphical view]
SUPFAMSSF54117. SSF54117. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP78423.
GeneWikiCX3CL1.
GenomeRNAi6376.
NextBio24772.
PMAP-CutDBP78423.
PROP78423.
SOURCESearch...

Entry information

Entry nameX3CL1_HUMAN
AccessionPrimary (citable) accession number: P78423
Secondary accession number(s): O00672
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: May 1, 1997
Last modified: March 19, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM